Toronto, ON – J.P. Arencibia hit a three-run home run, while 4, in the finale of a four-game set from Rogers Centre.
David Cooper finished with three hits and drove in two runs for the Blue Jays, who won three of four in the series.
"Taking three out of four against a team that's near the top of the division is huge," said Arencibia.
Ricky Romero (14-10) worked 6 2/3 innings for the victory, allowing five hits and three runs with three walks and striking out seven.
Marco Scutaro went 3-for-4 and notched two RBI for the Red Sox, who lost for the sixth time in eight games but remained 2 1/2 games back in the AL East after the Yankees lost in Baltimore earlier Thursday.
Andrew Miller (6-3) was tagged in defeat for five runs on eight hits over five full frames.
Encarnacion's one-out solo shot made it 5-0 in the third, and Romero didn't get into trouble until the seventh -- departing after Jacoby Ellsbury's two- out double to score Jason Varitek, who walked with one down.
Casey Janssen served up a two-run single to Scutaro to get the Sox within 5-3, but Thames hit a one-out homer in the bottom of the inning to give the Jays a three-run edge.
Brett Lawrie's one-out double in the eighth turned into Toronto's seventh run of the game when Cooper drove him in with a double.
Varitek greeted Frank Francisco with his 11th homer of the season in the ninth, then two batters were retired before Ellsbury reached on Toronto second baseman Kelly Johnson's fielding gaffe. Scutaro singled, but the game concluded in the Jays' favor when Dustin Pedroia fanned swinging.
The Jays jumped on Miller for four runs in the second. Johnson reached on a leadoff infield hit, Lawrie added a single and Cooper's base hit scored Johnson. Arencibia then launched a mammoth three-run shot to the third deck in left.
"Other than that big inning, I felt pretty good," said Miller. "That one inning just really blew up."
Toronto has won seven of 16 meetings, with a final two-game series slated for Fenway Park from September 13-14...Boston upped its MLB-best road home-run mark to 99...Romero, who has only lost once since mid-July, had been 2-6 with an 8.08 earned run average in 11 starts against the Red Sox prior to Thursday.