Phelps struck out Edwin Encarnacion looking to end the Blue Jays' threat without yielding a run.
"That's probably the biggest play of the game when you look back on it," Girardi said. "They had some momentum and you're in a tough spot, 3-2 on Encarnacion, and all of a sudden, you get a big pickoff and it helps you relax a little bit."
The Blue Jays were unsuccessful on a challenge in the eighth inning.
With one out and the bases empty, Dioner Navarro hit a ground ball to second baseman Roberts and was called out at first by umpire Chris Conroy.
Blue Jays manager John Gibbons challenged the ruling on the field -- because he thought Yankees first baseman Mark Teixeira pulled his foot off the bag -- down by two runs and with a chance to bring the potential tying run to the plate. But the call was ruled to stand.
Matt Thornton, who relieved Shawn Kelley after Navarro's at-bat, retired Juan Francisco on a popout to third to end the inning.
Jamal Collier is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.