With the game tied at 1, the bases loaded, two outs and a full count, Saunders hit a chopper to first and narrowly outraced pitcher Tony Sipp, who was covering the bag. The batters were running on the pitch, allowing two runs to score. The play was upheld after a brief replay review.
Jose Altuve homered on the game's first pitch for the Astros, who have lost three in a row.
Dominic Leone (0-1) pitched 1 2-3 innings for his first major league win in 16 appearances, and Fernando Rodney pitched a perfect ninth for his 12th save.
Houston starter Jarred Cosart (3-4) had kept Seattle's offense largely bottled up until the seventh inning.
Dustin Ackley and Stefen Romero led off with singles and Cosart walked Nick Franklin to load the bases with no outs. Cosart struck out Mike Zunino before giving way to Sipp, who got pinch hitter Cole Gillespie to pop up before Saunders' hit.
Cosart gave up three runs on five hits and four walks over 6 1-3 innings. He struck out six.
Seattle starter Roenis Elias pitched into the sixth inning, allowing three hits, with the only run coming on Altuve's leadoff homer. Elias struck out six, walked four and pitched out of jams a couple times early the first two batters reached in the second and third innings before settling down.
Altuve took Elias' opening pitch deep into the visitor's bullpen in right field for his second home run. It was Altuve's third career leadoff homer and first this season.
The Mariners scratched out a run in the bottom of the first. James Jones led off with a walk, advanced to third on Saunders' single and scored on Robinson Cano's sacrifice fly to center.
NOTES: Houston OF George Springer was held out of the lineup after injuring his hip while getting picked off in the ninth inning Wednesday. Astros manager Bo Porter said Springer could be back as soon as Friday. ... Seattle OF Logan Morrison (strained right hamstring) will begin a rehab assignment with Triple-A Tacoma on Friday, and LHP James Paxton (strained back muscle) will make a rehab start with Tacoma on Saturday. ... The Mariners signed RHP Todd Coffey to a minor league contract. ... Seattle CF James Jones singled in the third inning to extend his hitting streak to 12 games. Jones has at least one hit in all 13 of his major league starts.