After a two-run Baltimore seventh, Kenny Wilson stole third as Ryan Goins walked in the ninth. Luis Exposito then threw the ball away, and Wilson scored. Three batters later, a wild pitch by Adam Russell allowed Goins to cushion Toronto's lead.
But with two outs and runners on the corners, Flaherty took three balls and two called strikes against Neil Wagner before homering to right field, capping a game in which the two teams combined for 28 hits.
Orioles starter Jason Hammel struck out four and allowed a run on five hits and a walk over 2 1/3 innings in his second Grapefruit League outing. Mark Hendrickson recorded two outs after that, with prospect Mike Wright charged with a run over two innings of work.
"Still [throwing] a lot of fastballs," Hammel said of his early spring plan. "Want to stay on top of the two-seamer. I'll make sure that's where it needs to be, because that was a huge help last year. Change-up, I've been working on, too, but just throwing strikes and getting ahead of guys. I've been able to do that so far."
Steve Pearce continued his strong spring showing for the Orioles with an RBI double, while Nolan Reimold reached base three times, including a leadoff home run. Reimold, who served at designated hitter, has gone deep twice this spring, with Thursday's run coming off Blue Jays starter Mark Buehrle.
Buehrle went two innings and walked three, surrendering only Reimold's homer, in his second spring start against the Orioles. "Got my work in," said Buehrle, who threw 44 pitches. "I was a little more wild than I wanted to be, but I was kind of adjusting from the bullpen mound to the game mound and was a little off. But I felt great, the pitch count is all that matters."
Justin Germano followed Buehrle and allowed five runs (two earned) on four hits over two innings.
Up next for Blue Jays: Right-hander Josh Johnson will take the mound Friday afternoon when the Blue Jays visit the Braves in a 1:05 p.m. ET start at Champion Stadium, with an exclusive webcast on bluejays.com. Johnson will be followed on the mound by Steve Delabar, Esmil Rogers, Jeremy Jeffress, Tyson Brummett and Chad Beck. This marks the third consecutive road game for the Blue Jays, and it was not immediately clear which position players would be making the trip.