Joe Thornton had assists on both goals in the Sharks' second straight victory.
The victory gives the Sharks 111 points and a four-point lead over the idle Detroit Red Wings for the best record in the NHL.
Despite the loss, Calgary leads the Northwest Division with 92 points -- but its lead over second-place Vancouver is just one point. Calgary has six regular-season games to play while the Canucks have seven.
Boyle opened the scoring at 6:11 of the first period with the Sharks enjoying a two-man advantage. The Flames got the equalizer when Iginla scored from the left circle at 15:09 of the first.
Cheechoo picked up a carom of a Brad Lukowich shot and scored the decisive goal at 12:24 of the second.