Kiprusoff had been out of action since Feb. 5, but he was sharp in his comeback while the Flames were winning their second in a row.
The contest was deadlocked at 1-1 heading into the final period, but Kiprusoff was perfect during the closing 20 minutes while Blake Comeau, Jarome Iginla and Curtis Glencross were scoring for Calgary.
Comeau delivered the go-ahead goal 2:57 into the period, his first of the season.
Thomas Greiss allowed three goals on 25 shots. The Sharks had won three of their previous four.