Joba Chamberlain struggled with his control, walked off the mound in the third inning and threw his glove in the dugout.

His first major league start was a memorable one, all right. Just not for the reasons he’d hoped.

Chamberlain lasted just 2.1 innings and Roy Halladay held the Yankees in check despite some control problems of his own, leading the Toronto Blue Jays to a 9-3 victory last night.

Alex Rios extended his hitting streak against the Yankees to 24 games and David Eckstein had three RBIs for Toronto, which patiently concentrated on Chamberlain’s pitch count and forced New York to use six pitchers total.

Halladay (7-5) won his fourth straight decision and improved to 5-1 with a 2.58 ERA in his last seven games. He allowed two runs and six hits in six innings.

The former AL Cy Young Award winner got off to a rough start but quickly settled down and improved to 11-5 with a 3.03 ERA against New York.

Halladay was around long after Chamberlain departed from his much-anticipated start.

A sellout crowd of 53,629 that included Chamberlain’s father, Harlan, roared as the hard-throwing right-hander was introduced with the starting lineup and gave the youngster a standing ovation before he threw his first pitch.

His initial offering to leadoff hitter Shannon Stewart was a ball — a sign of things to come. Chamberlain touched 101 mph on the Yankee Stadium scoreboard but walked three and threw 38 pitches in the first as Toronto took a 1-0 lead on Rios’ groundout.

Chamberlain retired the side in order in the second and got Marco Scutaro to fly out to right to begin the third. But Rios walked on four straight balls, and manager Joe Girardi removed the 22-year-old after 62 pitches, about what the Yankees had planned to limit him to.

Dan Giese (0-1) relieved and allowed a run in 3.2 innings.

Chamberlain walked off the mound and sheepishly removed his cap to acknowledge the cheering crowd as he approached the dugout. He threw his glove down as he climbed down the steps and sat down with a dejected look on his face.

“It was the first step, that’s all,” said team co-chairman Hank Steinbrenner, who watched the game in his office at the Yankees’ facility in Tampa, Fla. “Again, he’s 22. This was the first step. We’re looking at a 10 year or more career.

“Tonight was a creation of the media. If this had been a first start for any other pitcher on any other team, it wouldn’t have been such a big deal.”

Chamberlain, the 41st overall pick in the 2006 amateur draft, was converted to a reliever last year to help the Yankees bridge the gap to closer Mariano Rivera. He made his major league debut at Toronto on August 7 and went 2-0 with a 0.38 ERA in 19 games.

Rios extended his streak against the Yankees with a seventh-inning single. It’s the second-longest active streak against one team in the majors and the longest against New York since Charlie Gehringer’s 31-game streak for Detroit from 1935-36, according to the Elias Sports Bureau.

Derek Jeter singled in the ninth inning to tie Mickey Mantle for third on the Yankees’ career list with 2,415 hits.