Matos homered to open the fourth off Toronto starter Cory Lidle to provide a 1-0 lead for rookie Matt Riley, who tossed five scoreless innings in his second start of the season.
Riley lost a chance at the win when John Parrish allowed the tying run to score on a wild pitch with two outs in the seventh.
Matos sparked the eighth when he reached on a one-out infield single off Lidle (12-14).
Kerry Ligtenberg (3-2) got the win. Jorge Julio tossed a scoreless ninth for his 35th save.
Rookie Reed Johnson extended his hitting streak to 17 games for the Blue Jays.