Home-plate umpire David Rackley, trailing the runner on an umpires' shift, ruled that Reyes beat the tag and Pujols immediately motioned to manager Mike Scioscia to challenge the call.
Replays showed Pujols' glove tagging Reyes on the ribs before his hand made contact with the bag and the call was overturned, making the Angels 9-for-17 in challenges this season.
Reyes' single was Toronto's fourth hit of the game but the score was 0-0 after three innings.
The Angels were also on the winning side of a challenge by Toronto's John Gibbons in the seventh inning.
Erick Aybar grounded a ball deep into the hole at short, where Reyes gathered the ball and threw to first. Aybar beat the throw, which was confirmed by a video review.
Matthew DeFranks is an associate reporter for MLB.com. Follow him on Twitter @MDeFranks. This story was not subject to the approval of Major League Baseball or its clubs.