Jakubauskas managed just one perfect inning and allowed at least one runner in scoring position in the other five. He was pulled after giving up a single and a one-out walk in the sixth. Reliever Michael Gonzalez struck out a batter, walked another and induced an inning-ending groundout to limit the damage.
The Orioles jumped on the board first when J.J. Hardy led off the game with a single and moved to third on a single by Markakis, who was caught in a rundown and tagged out while trying to get to second.
Jones followed with a sacrifice fly to center for the 1-0 lead against Carlos Villanueva, who retired 16 of the next 21 batters he faced. Villanueva was not charged with another run until he was out of the game.
He left in the seventh, after Luke Scott's bunt single to third base -- the second of the night for the left fielder, who took advantage of the left-side opening created by a right-side defensive shift -- and Reynolds' walk.
Jays reliever Jason Frasor entered and threw a wild pitch that moved the runners to second and third. Andino hit a sacrifice fly to right, and Hardy followed with an RBI double to cut the score to 4-3. Frasor got Markakis and Jones to ground out.
The Jays tacked on a run in the seventh when Aaron Hill hit a solo homer against Jeremy Accardo, who was making his return to Toronto after five seasons with the Blue Jays. It could have been worse, but after J.P. Arencibia broke a 0-for-12 skid with a leadoff double, he was thrown out by Wieters while attempting to move to third on a wild pitch.
Hill's homer was the only run allowed by the Orioles' bullpen -- Jim Johnson threw two scoreless innings -- until Lind crushed Uehara's final pitch and ended the three-hour, 47-minute marathon.
The Orioles have dropped three consecutive games after winning four straight last week.
"It could have come out different, but that's the way the game goes, it goes up and down," Andino said. "We've got to put that behind us."