The Mariners trailed by 1 entering the eighth before Shed Long Jr.'s run-scoring single tied it at 5 with one out.
Long stole second base with two outs before Lewis, who homered in the first two games, knocked a ball thrown by Chris Devenski (0-1) into right field to score two and put the Mariners on top.
Seattle went 1-18 against Houston last season and lost the first two games of this season to extend the skid.
Houston starter Zack Greinke came two outs from a no-hitter in his last regular season start, which was against Seattle on Sept. 25. On Sunday, Lewis spoiled his bid much earlier, singling with two outs in the first.
The Astros cut the lead to 1 in the bottom of the inning when Bregman hit an RBI double to left field but was thrown out trying to stretch it into a double to end the inning.
Mallex Smith and Long both hit RBI doubles in the fourth to extend the lead to 4-1.
The Astros loaded the bases with no outs in the fourth with two walks and a single by Brantley.
Martin Maldonado then sent a ball skipping down the third base line for a single that scored two to put Houston on top 5-4 and end Kikuchi's day.
Maldonado has five hits and six RBI in the first three games. He's the first MLB catcher to have six or more RBI in the first three games of a season since Brian McCann also had six in 2007.
Kikuchi yielded five hits and five runs with four walks in 3 2/3 innings.
Greinke allowed four hits and three runs while walking two in 3 1/3 innings.
Astros: INF Aledmys Díaz, who is on the 10-day injured list with a groin strain sustained in the opener, said it was between a Grade 1 and Grade 2 strain and he wasn't sure how long it would keep him out.
Seattle's Kendall Graveman will make his first appearance in 807 days when he starts against Josh James when the series wraps up Monday. Graveman last pitched on May 11, 2018 and missed the rest of that season and last season recovering from Tommy John surgery. James returns to the rotation after spending last season in the bullpen.
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