The Flames scored all of their goals in the final period to win their second straight and climb over Colorado and out of last place in the Northwest Division.
Trailing by one to start the third, Lee Stempniak and Curtis Glencross scored power-play goals 1:26 apart to give Colorado the lead. Both goals came with T.J. Galiardi serving a double-minor penalty for high-sticking.
Galiardi tied it for the Avalanche 9:58 into the period, but Jokinen gave the Flames the victory by putting a wrist shot past Jean-Sebastien Giguere.
Miikka Kiprusoff needed to make just 16 saves for Calgary. The Flames have won each of the last nine meetings with Colorado, four of them this season.
Giguere stopped 32 shots. Colorado won its first six road games this season, but has gone 0-6-1 away from home since then.