Markakis also scored twice in a victory that ended a five-game losing streak.
Nolan Reimold, Felix Pie and Ty Wigginton each had an RBI for the Orioles.
David Hernandez (3-2) was the winner, yielding a run and five hits over seven innings.
Jed Lowrie and Dustin Pedroia drove in the Red Sox runs.
Loser John Smoltz (1-4) was tagged for six runs and nine hits in five innings.
The Red Sox have dropped six of eight and trail the first-place New York Yankees by 2 1/2 games in the American League East. The Yankees beat Oakland 7-5 Sunday.
Copyright 2009 by United Press International.