The Blue Jays, who had lost six straight at home before coming to Oakland, headed to Anaheim just two games behind the A's in the wild-card race.
Fernandez, who had been hitless in his previous three games for the first time this season, doubled to lead off the Blue Jays' two-run second. He had a two-run double as Toronto added five in the fourth, and an RBI double in a two-run sixth.
"He's swinging the bat like it's a magic wand," A's manager Art Howe said. "He can flat-out hit. He uses the whole field. It's hard to pitch him, inside or outside."
Batista had an RBI double in the second and a solo homer in the fourth. Batista, who had 10 homers while playing for Oakland in 1996-97, has 25 this season including 20 for the Blue Jays.
McRae hit a two-run homer in the fourth, his second since joining the Blue Jays in a trade earlier this month. Shawn Green had an RBI double in the sixth.
David Wells (12-8) got his first win since July 22, allowing four runs and eight hits in 5 2-3 innings. He said he tried to focus on his performance, not on the Blue Jays' recen troubles.
"Worrying about where we are in the standings, that's not acceptable. I just have to go out and get outs," Wells said. "I don't want to apply any pressure on myself."
Kevin Appier (12-11) lasted just 3 2-3 innings, allowing seven runs but only three earned, in by far his shortest start since joining the A's in a July 31 trade. He has lost his last two starts after winning his first three starts for Oakland.
Appier was bothered by a strained muscle in his right leg that has been a problem for him all season. He left the A's clubhouse during the game to see a doctor.
"It's very painful, it's more painful than it sounds. It can be like a toothache some days, and throbbing the next," said A's trainer Larry Davis. "He's had it all year and today it was bothering him."
Even though the game was between teams battling for the AL wild card, it drew an attendance of just 10,047. Several fans booed when the figure was announced.
"Nothing changes. We're past worrying about how many people are going to come out, whether it be 30,000, 40,000 or 10,000," Howe said.
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