Trailing 5-3 entering the seventh, Cooper led off with a solo shot off Orioles starter Tommy Hunter (3-4). One out later, Loewen tied the score with another bases empty-clout.
Mike McCoy (2-for-3, three runs scored) followed with a double and Eric Thames singled to chase Hunter. Jose Bautista then delivered a go-ahead sacrifice fly off Willie Eyre to hand the Blue Jays the rubber match of a three-game set.
Joel Carreno (1-0) collected his first major-league win with a scoreless seventh inning and Frank Francisco picked up his 14th save in the win.
Nick Markakis went 2-for-4 with a two-run single for the O's.