The Reds carried a 9-5 lead into the ninth, but All-Star closer Aroldis Chapman walked four straight batters before he was replaced by J.J. Hoover. Pinch-hitter Wilin Rosario then hit a sacrifice fly to trim Cincinnati's lead to two.
After Charlie Blackmon flied out, Stubbs drove a 1-0 pitch from Hoover (1-9) into the seats in left for his 12th homer. It was Stubbs' third career game-ending homer and first with the Rockies.
Rex Brothers (4-5) picked up the victory despite allowing a pair of runs in the top of the ninth. Nolan Arenado tied a career high with four hits for Colorado. He also had a leadoff walk in the ninth.
Stubbs finished with three hits against his first major league team, and then was doused with ice water by a teammate during an on-field interview after the game.
The doubleheader was set up by Saturday night's water main break outside Coors Field that left the ballpark without running water and forced the game to be pushed back one day. The ruptured water main was repaired by city crews overnight.
Charlie Blackmon and Corey Dickerson also went deep for the Rockies.
The Rockies' Michael Cuddyer, who won the NL batting title last season, went 1 for 5 in his return from a left shoulder fracture. He was injured June 5 against Arizona when he dove for a sharply hit grounder while playing third base.
A brief thunder shower prompted a 21-minute rain delay in the first.
Reds: 2B Brandon Phillips (torn left thumb ligament) continued his minor league rehab stint with Class A Dayton on Sunday at Bowling Green. Phillips began the assignment Friday at Triple-A Louisville, going 0 for 2 with a walk against Indianapolis.
Reds: RHP Mike Leake (9-11) is slated to pitch Monday's series opener at St. Louis, where Cincinnati has gone 1-10 in its last 11 series.
The game was played with balls embossed with the No. 17 in recognition of Todd Helton, who wore that number during a stellar Colorado career and saw it retired during a pregame ceremony. He's the first player in the team's history to have his number retired.