Oakland avoided a series sweep as Manaea (2-2) gave up just two hits and struck out four. It was the third time in four starts this season he has lasted at least seven innings.
Lowrie provided all the offense the A's needed with his fourth homer in the first inning. Blake Treinen finished with a four-out save.
Taylor Motter homered for the Mariners, who had won four in a row.
Manaea has been solid in every outing this season, allowing two runs or fewer each time. He held Seattle scoreless until Motter's fifth-inning homer.
The only other time a Mariners runner advanced past first base against Manaea was in the first, when Robinson Cano walked with two outs and moved to third on a wild pitch and a passed ball. Manaea got Nelson Cruz to fly out, stranding Cano, and Seattle's offense was largely shut down the rest of the day.
Hernandez (2-2) also was effective, but he couldn't match Manaea.
The longtime ace worked into the seventh inning for the first time this year, giving up five hits in 6 1/3 innings. He retired 13 in a row after Lowrie's homer, and struck out seven without issuing a walk.
In the first inning, Marcus Semien singled and then appeared to get picked off first base before a balk was called on Hernandez. After the umpires huddled, the balk was called off and Semien returned to first. Lowrie followed with his homer to right field, giving Oakland a 2-0 lead.
Oakland loaded the bases with one out in the eighth but was unable to score an insurance run. Chasen Bradford struck out Matt Olsen and got Matt Chapman to line out to left field, escaping the jam.
Athletics: INF Chad Pinder (hyperextended left knee) began a rehab assignment with Class A Stockton on Saturday, going 1 for 5. Pinder is eligible to return from the 10-day disabled list Monday. "Looks like he's on track to come back here pretty quick," manager Bob Melvin said.
Mariners: C Mike Zunino (oblique strain) will start a rehab assignment Monday at Class A Modesto. Seattle manager Scott Servais said Zunino will likely play three rehab games there before rejoining the Mariners. . OF Ben Gamel (oblique strain) might rejoin the team in the next few days, Servais said.
Athletics: RHP Daniel Mengden (1-2, 6.19 ERA) will start against the White Sox on Monday. Mengden is 0-10 in 13 career starts in Oakland.
Mariners: LHP James Paxton (0-1, 5.74) opens a four-game series Monday against the Astros. Paxton tied a career high with 10 strikeouts in his last start at Kansas City.