Nick Tarnasky netted the only Amerks goal early in the first period, tipping in a Mark Mancari shot on the power play.
McMillan answered by poking in a rebound late in the first and then Houston took the lead when Justin Fontaine one-timed a shot from the slot immediately after a faceoff.
From there, the Aeros muddied the game and scoring chances were scarce for either team. Matt Ellis had the best chance to tie for the Amerks, but his point blank wrister was snuffed by the glove of Matt Hackett.
McMillan added an empty net, shorthanded goal with a minute remaining to put the game away.
The result soured the inductions of Rich Funke and Dane Jackson to the Amerks Hall of Fame before the game. Funke is a long-time Rochester broadcaster who recently retired. Jackson played five seasons with the Amerks from 1995-98 and 1999-2001. He's the last man to captain Rochester to a Calder Cup.