Bourque has six goals this season, five in his last two games. He also had an assist to go along with his hat trick in Friday's 6-2 win against the Blue Jackets.
Jarome Iginla and Craig Conroy also scored for Calgary. The Flames have won four of their last five games to improve to 5-3-0 and have tallied 10 goals in their last two games after scoring 11 in their first six.
"Whether we scored or not we were playing well," Calgary coach Brent Sutter said. "We were able to have the emotion level we wanted to have. We took advantage of the opportunities and made the most of them."
The Sharks, coming off a 6-1 victory in Edmonton on Saturday night, dropped to 3-3-1 with their first road loss of the season.
"They wanted to get on us early, and we knew that was their game plan," San Jose captain Joe Thornton said. "We couldn't stop them. The first 10 minutes dictated the whole night. It wasn't good for us."
Bourque has made a big impact since his return from a head injury. He has three winning goals in four games, tying him for top spot in the NHL with Chicago's Patrick Sharp.
"Anytime you're scoring, you want to have the puck on your stick," Bourque said. "I feel like I could make plays happen right now. We're just getting the puck deep and coming up the middle of the ice with speed. It seems to be pushing the 'D' back and it's giving us a lot of room and a lot of time with the puck to find other guys open."
Kiprusoff was busiest in the second period, when San Jose peppered him with 12 shots. But the Flames' goaltender stopped them all to keep the Sharks off the scoreboard.
During one stretch on a power play, San Jose put three shots on goal, but Kiprusoff calmly turned them all aside -- including a sharp pad stop off Ryan Clowe.
"They did start shooting a little more in the second," Kiprusoff said. "But we played smart. It's pretty nice when you have a lead like that. We knew we were going to get more chances if we just waited."
The Sharks managed to outshoot the Flames by a 9-6 margin in the third period, but it was much too late. San Jose has now been outscored 21-19 in its first seven games.
"In the first period, there probably could have been two pucks on the ice and we wouldn't have had either one of them," Sharks coach Todd McLellan said. "We weren't playing the way we're supposed to play as far as the system went, and it was very disappointing."
Material from wire services and team media was used in this report.