Iwakuma (6-3) scattered five hits, didn't walk a batter and struck out seven for his fourth win in five starts.
Josh Kinney worked out of a two-on, one-out jam in the seventh, sending the Mariners into the ninth with a 2-0 lead.
But Wilhelmsen got Aybar on a game-ending flyout to notch his 22nd save.
Jesus Montero and Carlos Peguero each socked a solo homer for Seattle, which avoided a three-game sweep.
Angels starter Jared Weaver (16-4) allowed eight hits and walked four over 5 1/3 innings, surrendering a pair of runs.
Los Angeles fell 3 1/2 games off the pace for an American League wild card spot.