Iwakuma (4-2) limited the Braves to six singles, did not walk a batter and struck out seven to bounce back from losses in his previous two outings.
Kyle Seager and Cole Gillespie each drove in a run as the Mariners tied a season high with their fifth straight win.
Mike Minor (2-4) struck out 10 but was saddled with the hard-luck loss after giving up one run on five hits over seven innings.
Atlanta dropped both games in this brief series and fell to 0-6 in interleague games this year.
The Mariners broke a scoreless tie in the fourth inning when Gillespie singled through the left side with two away to knock in Robinson Cano, who led off the frame with a base hit.
Seattle squandered several scoring chances before finally adding on against Atlanta's bullpen in the eighth. Luis Avilan relieved Minor to start the frame, and Stefen Romero rolled one into the right-field gap and legged out a one-out triple. Seager followed with an RBI single.
Iwakuma provided Seattle's relievers with some much-deserved rest after they tossed six shutout innings in Tuesday's win.
He retired 12 straight at one point and quickly erased Evan Gattis' leadoff single in the seventh by getting Chris Johnson to bounce into a double play.
Yoervis Medina tossed a 1-2-3 eighth behind Iwakuma, and Fernando Rodney did the same in the ninth to post his 16th save.