Yates, making his second consecutive start for the injury-depleted Texans, found Walter over the middle with a 6-yard TD pass on the game's final play, handing Houston (10-3) the AFC South championship following Tennessee's loss to New Orleans Sunday.
The winning play was set up thanks to a pass interference call on the Bengals with 12 seconds to play and helped rally the Texans from a 19-10 deficit late in the third quarter.
Yates finished 26-of-44 through the air for 300 yards, two touchdowns and interception while subbing for the injured Matt Leinart.
Owen Daniels made seven grabs for 100 yards while Kevin Walter added six receptions and a score for 76 yards in Houston's win.
Andy Dalton completed 16-of-28 passes for 189 yards and a score for the Bengals (7-6), who dropped their second straight.