John Patrick Shanley’s new play arrives right on time. The day before Thanksgiving, New York gets a show that deserves our giving thanks. Intelligent, provocative, and viscerally exciting, Mr. Shanley’s play, which opened last night at the Manhattan Theatre Club, also boasts a couple of the most thrilling performances in recent memory. If this show doesn’t end up on Broadway, I don’t know what Broadway’s for. So three cheers for “Doubt.”

And three cheers for doubt. “What do you do when you’re not sure?” runs the first line of the play. Father Brendan Flynn (Brian F. O’Byrne) is delivering a homily to the faithful at St. Nicholas Parish in the Bronx. It is 1964, and Father Flynn seems kind, gracious, decent. Yet the very next scene raises the possibility that the good father has been interfering with one of the eighth-grade boys. The boy’s teacher, young Sister James (Heather Goldenhersh) takes her suspicion to the principal, the forbidding Sister Aloysius (Cherry Jones). She has suspicions of her own. What they don’t have is proof.

We’ve been over this terrain, of course. Earlier this season, The New Group staged “Sin (A Cardinal Deposed),” a docudrama about Cardinal Bernard Law and the abuse cases in the Boston archdiocese. Just last week, Pedro Almodovar’s new film “Bad Education” opened. It, too, concerns a priest who molests a student, though the circumstances and import are much different. (Mr. Almodovar has his own purposes.)

Mr. Shanley has surpassed all prior attempts to deal with this subject. With seriousness and humor, he has written what he calls “a parable.” It is, on the most elementary level, the story of a school administrator trying to crack a case, to protect her students. But it resonates because it works on all the other levels, too.

This being a Catholic school, and the three central characters being clergy, the play takes on a spiritual dimension. (With four actors and only 90 minutes of stage time, it’s like a compact spiritual symphony.) Sister Aloysius knows she should take her concerns to the monsignor, but he is “oblivious” and “otherworldly in the extreme.” She will have to seek the truth by her own lights, relying on some mix of experience, belief, and intuition. It doesn’t take much imagination to see this as a metaphor for the predicament of all believers, who try to do right without being able to consult a higher power. Doubt is an existential state for those honest enough to acknowledge it.

Did the priest go wrong, or is Sister Aloysius just staging a witch-hunt? Did she find evil or is she inventing it? Mr. Shanley shows great skill in keeping the questions unanswered for so long. After all, Sister Aloysius wouldn’t get along with Father Flynn in the best of circumstances. In her black habit and bonnet, she is the picture of a strict and traditionally conservative nun. She is opposed to satisfaction, reassurance, and ballpoint pens; and in favor of skepticism, the dying art of penmanship, and the pedagogical usefulness of terror. “Innocence,” she tells sweet, simple Sister James, “is a form of laziness.”

But then it was a conservative time. Sister Aloysius comes from a school that insists a priest and nun cannot be alone together. Hers is the Catholicism that sees temptation on every side, and combats it with righteous vigilance. Father Flynn, by contrast, represents a new order. He welcomes the liberalizing changes of Vatican II and feels that clergy should play a larger role in parishioners’ lives. He wears his fingernails scandalously long, dares to use sugar in his tea, and thinks that the boy in question, Donald Muller, deserves some slack because he’s the first black student in the school. (Sister Aloysius says he should get the exact same treatment as anyone else.)

When Father Flynn defends himself to Sister James, he sounds like any liberal Catholic talking about any church issue, even today. “Have you forgotten that was the message of the Savior to us all? Love. Not suspicion, disapproval, and judgment. Love of people.” See what Mr. Shanley is up to? He makes the liberal, the person who believes all the “right” things, do (or seem to do) all the wrong things. The challenge flung at the audience’s pieties is splendid, nearly Trilling-esque.

All this may seem too schematic: old vs. new, tradition vs. progress, liberal vs. conservative. But at a crucial moment, late in the play, those terms shift. Mr. Shanley grants his characters the capacity to surprise. They cannot be reduced to holders of positions, or mouthpieces of philosophies. They are people. Where Mr. Shanley does slip a bit is a certain mechanical way of supplying details here and there. Sister Aloysius’s many foibles come across in almost list form, and a late scene with Donald’s mother (Adriane Lenox), feels rushed, forced.

Distilling this kind of environment to 90 minutes of dialogue poses real difficulties, to be sure. Catholic school has its moments of explicit instruction, but operates more by letting impressionable young minds marinate in a kind of moral solution over many years. All in all, Mr. Shanley captures it pretty well – trust me.

The arresting MTC production owes much to director Doug Hughes. His pace is supremely confident, and the use of the stage is assured. John Lee Beatty’s set consists of a permanent school courtyard, into which slides the principal’s office, the locker room, or nothing at all, for the scenes when Father Flynn addresses us in his green and gold robes.

Sister Aloysius and Father Flynn spend the entire play maneuvering around one another, but only come face-to-face twice. The first time, Sister James is present; the second is purely mano-a-mano, just two great actors squaring off with some exceptionally pungent dialogue. The upper hand keeps changing, and the tension keeps rising. When was the last time a play made your heart race? I don’t want to give away details before you’ve seen it – and you must see it. Suffice it to say that Cherry Jones and Brian F. O’Byrne trying to out duel one another may be the closest approximation to heaven that the New York theater provides.

For all her bold statements about iciness and skepticism, Ms. Jones gives Sister Aloysius little spots of warmth. She is stubborn, to be sure. But in the fraught final scene, she finds a moving depth. Mr. O’Byrne avoids all outward signs of villainy. To the end he insists he has done nothing wrong – which, in his own mind, is true. Even more than his turn as a child killer in last year’s “Frozen,” his performance mesmerizes. Ms. Goldenhersh holds her own with these two – no small feat. She is affecting when she quavers: a young woman constantly on the rack, trying to do what’s right without causing harm.

Sister James frets about what they’re doing to flush out Father Flynn, but Sister Aloysius is unyielding. “When you take a step to address wrongdoing, you are taking a step away from God, but in His service.” (What a provocative statement – how many misdeeds could that statement justify?) The final triumph of Ms. Jones’s performance is that we see the cost exacted by her actions. Doubt is vanquished by certainty, only to be replaced by new and graver doubts.

Mr. Shanley doesn’t sentimentalize Sister Aloysius, but he treats her with a great, generous sympathy. If I read him right, she is a kind of hero in this morally compromised world: Doubt can be painful, and can lead to despair, but a moral life requires us to reckon with it. As if the play isn’t tribute enough, Mr. Shanley included a gracious note about women like Sister Aloysius in the program. It bears reprinting in full:

“This play is dedicated to the many orders of Catholic nuns who devoted their lives to serving others in hospitals, schools and retirement homes. Though they have been much maligned and ridiculed, who among us has been so generous?”

On top of all the others, here is one more reason for thanks.

Until January 9 (131 W. 55th Street, between Sixth and Seventh Avenues, 212-581-1212).