Hernandez (13-7) threw 96 pitches in just 4 2-3 innings, his shortest outing since May 16 when he went 3 2-3 innings at Cleveland. He gave up five earned runs, 11 hits matching his season high walked one and struck out four.
It was the second straight loss for the 2010 Cy Young Award winner. He had been 9-1 with a 1.62 ERA in his previous 15 starts since June 17, with five shutouts, including a perfect game on Aug. 15.
The victory broke the A's three-game losing streak. They trail Texas in the AL West by 4 1-2 games. The A's, Yankees and Orioles are all within a half-game of each other on top of the wild card standings.
A.J. Griffin (5-0), in his 10th start his rookie season, went 5 1-3 innings to pick up the victory. He gave up one run and six hits, walking one and striking out seven.
Cliff Pennington had a season-high four hits for the A's.
Josh Donaldson drew a one-out walk in the fourth inning and was followed by a Stephen Drew single to set up Kottaras' three-run shot, on a 1-1 pitch from Hernandez. It was Kottaras' fourth home run.
The A's touched Hernandez for two runs in the fifth. Donaldson had an RBI double into the left-field corner, as Brandon Moss scored from first. Drew followed with a run-scoring single to right, ending Hernandez's night.
The A's pushed across an unearned run in the first. Seth Smith reached on a one-out single. With two outs, Yoenis Cespedes blooped a single to right but Thames overran the ball and Smith was waved home on the error.
The Mariners got that run back in the second. Michael Saunders led off with a single to center. With two outs, Luis Jimenez walked and Saunders scored on Brandon Ryan's single to right.
NOTES: The A's will start Dan Straily on Tuesday to fill the spot in the rotation for injured Brandon McCarthy, who was hit by a line drive Wednesday. Straily, who was with the big club earlier this season, was recalled from Triple-A Sacramento. "I think he has been through all the 'firsts.' He knows what it's all about up here," A's manager Bob Melvin said. "We're not afraid to throw some young pitchers out there. We have a lot young starters in the rotation right now. We'll just add him to that mix." ... The Mariners started CF Franklin Gutierrez and LF Saunders, a rare game in which both played. Each was coming off an injury while Gutierrez has been out most of the season with various injuries. "We've essentially got two center fielders out there, which is nice," Mariners manager Eric Wedge said. ... Jimerez, the Mariners' 30-year-old rookie callup, got his major league hit, a single in the fourth.