Lee Stempniak's power-play goal in the first period was all the offense for Calgary.
The Flames outplayed San Jose in the opening period with a 16-9 edge in shots, a couple of chances that went off the post and a Mikael Backlund breakaway foiled by Niemi.
San Jose recovered to outshoot the Flames 14-4 in the second period and took advantage of a loose defense around Kiprusoff to score three times from close range.
"That first period was a little bit of a shock, but after that the guys fell into it and you get into a rhythm," Marleau said. "It's going to be a learning curve, a little bit of rust for all teams.
"You try and get those points as quick as possible, especially with a shortened season."
As other NHL teams have done at home openers to soothe the feelings of fans after the lockout, the Flames discounted food, drink and merchandise Sunday. The stores at the Saddledome were doing brisk business 90 minutes prior to the game.
The Flames pressed in the third period with 12 shots to San Jose's six, but Niemi held off Calgary.
With Calgary's Curtis Glencross and Sven Baertschi serving coincidental minors late in the third period, Boyle scored a power-play goal on a two-man advantage with a minute remaining.
"We had everything in place for a great game but the bottom line, we played 40 minutes," Hartley said. "We have to show more consistency."
San Jose scored two power-play goals on six chances, while Calgary went 1 for 3.
"We weren't our best, put it that way," Thornton said. "We've still got a lot of work to do and we realize that, but starting on the road and getting the first win was huge."
The Sharks captain said the previous day, when most NHL teams were in action, felt like the eve of the postseason because he and his teammates were anxious to play.
"Everybody is kind of relieved it's back and hockey's back," Thornton said. "Last night, it kind of felt like playoffs were going to start because everyone was kind of gathered around watching hockey, which is a little bit strange."
The Flames were without offseason acquisitions Jiri Hudler and Roman Cervenka on Sunday. Hudler attended his father's funeral in the Czech Republic on Friday and Hartley did not know when the forward would return.
Cervenka, another Czech forward, has yet to be cleared to play because of anti-coagulant medication he took following the discovery of blood clots.
Sharks defenseman Brent Burns was out of the Sharks lineup with a "lower-body injury."
Forward Scott Gomez, recently bought out of his contract by the Montreal Canadiens, skated with the Sharks during their optional pregame skate Sunday.
Pavelski extended his streak of two points in San Jose season openers to four straight years. ... Calgary hosts the Anaheim Ducks on Monday before heading to Vancouver on Wednesday for three games in four nights to start the lockout-shortened season. ... San Jose is in Edmonton on Tuesday to face the Oilers. The Sharks don't play their home opener until Thursday against Phoenix.
Copyright by STATS LLC and The Associated Press
CALGARY, CANADA - JANUARY 20: Calgary Flames fans attend the first home game this season against the San Jose...