Masterson (7-8) tamed the Orioles on seven hits, issued a single walk and struck out six for the Indians, tossing 60 of his 92 pitches for strikes.
Vinnie Pestano recorded two outs in the eighth -- including a play on which Nick Markakis was thrown out at the plate on an Endy Chavez double -- and Chris Perez turned in a 1-2-3 ninth for his 27th save, securing the victory.
Choo's blast gave the Tribe a 2-0 lead in the third inning and Michael Brantley added an RBI single in the eighth as Cleveland avoided a four-game sweep at the hands of Baltimore.
Tommy Hunter (4-5) absorbed the loss, surrendering three runs on eight hits over seven frames.
Omar Quintanilla drove in the only run for the Orioles, whose five-game winning streak was snapped.