The Orioles handed Buehrle his second straight loss, knocking him around for eight hits and four runs in 6 1/3 innings while cutting Toronto's lead in the division to 3 1/2 games.
Kevin Gausman (2-1) picked up his second win in a row, allowing a run on five hits and three walks over six frames. The former first-round pick was coming off his first win as a starter Saturday against Oakland after being recalled from Triple-A Norfolk.
Buehrle (10-3) remained tied with Yankees rookie Masahiro Tanaka for the MLB lead in wins. He also lost to St. Louis on Saturday despite giving up just one run in seven innings, snapping a seven-start unbeaten streak
The scuffling Blue Jays have lost five of their last six on the heels of an 18-3 stretch.
Nick Markakis singled at the end of a six-pitch at-bat leading off the first inning for Baltimore and Young stroked a changeup over the left-field wall for his second homer of the season and a 2-0 Orioles lead.
They went up 3-0 in the second inning after Manny Machado doubled off the right-field wall to snap an 0-for-18 slump, went to third on Jonathan Schoop's sacrifice bunt and scored on Caleb Joseph's single.
The Blue Jays had just two hits before Juan Francisco hit a leadoff double in the fifth inning. He went to third base on Anthony Gose's sacrifice bunt and scored on Melky Cabrera's two-out single to get Toronto on the board and end a 19-inning shutout streak by Orioles pitchers.
Markakis knocked Buehrle out of the game in the seventh with an RBI double off the scoreboard in right field. Schoop, who led off the inning with a double, scored to make it 4-1.
The Orioles loaded the bases with one out in the eighth inning but Aaron Loup settled down after back-to-back walks to strike out Schoop and Joseph.
Zach Britton gave up a single to Steve Tolleson in the ninth inning but got Darin Mastroianni to ground into a double play to end the game and lock down his sixth save of the season.
The call was upheld after a Blue Jays challenge.