Polanco, who missed the NLDS opener with back soreness, played third base and hit second.
"He's feeling very good," Manuel said before the game. "He got OK'd and he told me he's fine. He said he feels a lot better."
Center fielder Shane Victorino moved into the leadoff spot, and shortstop Jimmy Rollins dropped from first to sixth.
"I wanted a couple right-handed hitters behind [Ryan] Howard in case they brought in a lefty," Manuel said of his decision to hit Jayson Werth fifth, Rollins sixth and Raul Ibanez seventh. "We can get some balance. Ibanez has been hitting the second half of the season, and especially against left-handers pretty good. But I liked that lineup the other day, and I like it now because of the fact they've got depth and left-handers in the bullpen."
Ibanez hit .303 with 10 home runs, 47 RBIs and an .853 on-base-plus-slugging percent from July 1 through the end of the regular season. He hit .295 against left-handers in that stretch.