Stubbs finished with three RBI and Miguel Cairo knocked in two runs for the National League Central-leading Reds, who were victorious for the 17th time in 19 games overall.
Mat Latos (9-3) won his second consecutive start, holding the Rockies to two runs on four hits over eight innings. The right-hander walked three and struck out eight.
Colorado starter Jonathan Sanchez (0-2) lasted just 4 1/3 innings, absorbing the loss. He coughed up six runs on eight hits.
Josh Rutledge belted a two-run homer for the Rockies, who fell for the ninth time in 11 contests.