Joba Chamberlain (1-0) worked a scoreless inning and Mariano Rivera got three outs for his second save.
With the score tied at 2 on a 42-degree night, Melky Cabrera opened the eighth with a single off Brian Wolfe (0-1). Scott Downs bobbled Johnny Damon's sacrifice bunt for an error that allowed Damon to reach safely, and Derek Jeter advanced both runners with a sacrifice bunt.
Abreu then dropped a soft single into center for his first RBI, making him 5-for-10 on the year.
Toronto put a runner on second with one out in the ninth, but Rivera retired Lyle Overbay and struck out Aaron Hill to end it.
The Blue Jays play their home opener Friday night, with Shaun Marcum on the mound against Boston knuckleballer Tim Wakefield.
Dustin McGowan kept the Yankees scoreless until the sixth, when they loaded the bases with none out. Damon dashed home on a wild pitch before Alex Rodriguez struck out, and Jason Giambi's sacrifice fly tied it at 2.
A 12-game winner last season, McGowan returned to the team hotel Wednesday because he wasn't feeling well - perhaps a 24-hour stomach bug, manager John Gibbons said.
But the 26-year-old right-hander, a member of Toronto's opening-day roster for the first time this season, looked plenty strong while going pitch-for-pitch with Hughes in a matchup of promising youngsters.
The 21-year-old Hughes, the youngest pitcher in the majors, featured a sharp curveball in his first outing of the season. He and McGowan both allowed two runs and four hits in six innings, with four strikeouts apiece.
The Yankees are counting heavily this season on three pitchers 23 or younger: Hughes, Chamberlain and Ian Kennedy, who starts Friday night against Tampa Bay.
Alex Rios' RBI single in the fourth extended his hitting streak against the Yankees to 23 games dating to September 2006, the longest by a player versus New York since Detroit Hall of Famer Charlie Gehringer had a 31-game run from 1935-36, according to the Elias Sports Bureau.
David Eckstein added an RBI infield single with two outs in the fifth, a ball that squirted out of a diving Rodriguez's glove at third base.
Blue Jays designated hitter Frank Thomas was ejected by plate umpire Bill Miller for arguing a called third strike to end the fourth. Thomas was replaced by Shannon Stewart.
