Veteran quarterback Kevin Kolb, who is competing with Manuel for the starting job, dressed but served as the emergency quarterback in the preseason opener after missing most of the week of practice.
Manuel did not throw an interception, but was credited with a fumble on a botched hand-off to running back C.J. Spiller that was recovered by the Colts.
However, Manuel led the Bills on a 95-yard drive with less than two minutes left in the first half, going 9-for-9 passing. Manuel's 17-yard touchdown pass to tight end Dorin Dickerson to cap the drive gave the Bills a 20-13 lead going into the second half.
"Here you are right before a half, 1:50, three timeouts left, and you're making decisions. Are we going to try to run out the clock? Are we going to go 2-minute? Hey, let's go 2-minute," Bills coach Doug Marrone said. "To do that is very impressive, no matter who you are."
Manuel also rushed for 28 yards on three carries, including a 24-yard scramble in the first quarter.
"My main thing was I wanted to operate the offense like coach (Nathaniel) Hackett has taught us and get all the other guys in position," Manuel said. "The veterans have done a great job of bringing me along and things like that. The main thing is just continuing to go out there and execute."
Jeff Tuel replaced Manuel at quarterback for the start of the second half.
Rookie wide receiver Marquise Goodwin had two long kickoff returns for the Bills, including a 107-yard return for a touchdown in the second quarter.
Defensive end Mario Williams (foot) and defensive tackle Kyle Williams (Achilles) both started for the Bills and played two series. Mario Williams sacked Colts quarterback Andrew Luck for a 10-yard loss on the Colts' second possession.
Luck finished 4-of-6 for 51 yards during his time in the game.
Information from The Associated Press was used in this report.