The veteran's 13-footer gave the Pacers a three-point lead and it turned out to be the last score of the game, with Ricky Davis and Paul Pierce both missing late shots for the Celtics.
With the best-of-seven Eastern Conference quarter-final all square at 1-1, the teams head to Indianapolis for Games Three and Four.
The 39-year-old Miller rebounded from a poor Game One, in which he scored just seven points as Boston won 102-82.
Miller, who plans to retire at the end of the playoffs, went 9-for-18 from the floor while playing a team-high 39 minutes.
The Pacers trailed by five points after three quarters, but Indiana held Boston to just 10 points in the fourth to nail down the win.
Stephen Jackson added 20 points for the Pacers, while Jermaine O'Neal chipped in with 13.
Pierce led all scorers with 33 points for the Celtics, who shot just 39 percent yet still held a seven-point lead with eight minutes remaining.
Antoine Walker added 19 points and seven rebounds for Boston, but no other Celtic managed more than six points.
