The three-time All-Star, who is batting .232 with six homers and 29 RBIs in 71 games this season, was in the seventh spot of the order for the first time this year.
"Due to the way we've played and the way Justin Turner's handled the second spot, [we] try to juggle the order a little bit so we don't have and exploit the other left-handed relievers on the other team," Mets manager Terry Collins said. "Don't exploit our left-handed lineup."
The Marlins have two southpaw relievers, Randy Choate and Mike Dunn. In Saturday night's lineup, the Mets had lefties Daniel Murphy and Jose Thole as well as switch-hitters Jose Reyes and Carlos Beltran.
On the season, Bay has 79 at-bats in the cleanup spot, 113 in the fifth slot and 67 sixth in the order.
"I know he doesn't care. I know he told me yesterday, 'I'm ready to play tomorrow' and I said, 'You're in there,'" Collins said. "I thought about the lineup today, who's pitching. I looked at all the variables and said, 'This is where I think he fits best in the lineup.'"
Collins cites what Bay did in seven games against the Dodgers -- two homers and six RBIs -- as something he hopes happens again to wake up Bay's bat.
"When he starts swinging the bat obviously we have to get him in the mix," Collins said. "When he does what he did in Los Angeles I've got to move him up in the batting order."