Joe Thornton added a goal and assist, while Joe Pavelski had three helpers for the Sharks, who have won two in a row and also scored six goals in each contest. It was San Jose's ninth victory in the last 11 games.
"We had a lot of movement and a lot of chances," Boyle said. "I had two great passes from (Pavelski) and was fortunate they went in."
Brian Boucher made 28 saves for San Jose in place of Evgeni Nabokov, who remains sidelined with a lower body injury.
Kris Versteeg netted a pair of goals for the Blackhawks, who have lost three in a row. Brian Campbell and Cameron Barker each finished with a goal and two assists in the loss.
"We played well, it was unfortunate how they scored at the end," Versteeg said. "They're a really big team and strong. It was a fast game and fun, also. We're a young team and have good energy; we're only going to get better."
Cristobal Huet made 25 saves for Chicago, which has dropped 12 consecutive games to the Sharks.
Chicago used a string of three goals to take a 5-4 lead into the second intermission, but San Jose tied the game shortly into the final stanza.
With the Sharks on one of their six power plays, they worked the puck to Boyle with a series of quick cross-ice passes. He got the puck and ripped a wrister into the right side of the net just one minute in.
The game remained tied until San Jose took another power play with 5 1/2 minutes left. Setoguchi got the puck near the center of the blue line and blasted a shot through traffic and into the net, giving the Sharks a one-goal lead with 4:15 remaining, and they held on for the win from there.
Milan Michalek got San Jose on the board just 42 seconds into the game after a faceoff, flicking the puck from the left circle past Huet into the right side of the net.
But at the 8:51 mark, Versteeg tied the contest after Boucher went to retrieve the puck behind the net on a San Jose power play. He didn't commit to a pass as Versteeg took the disc, skated out front and backhanded it in for an easy goal.
"As a goaltender, that's the last thing you want to do," Boucher said. "I thought we were making a line change, and we weren't. Then I tried to clear it and that didn't work either."
Thornton scored just 24 seconds later on the same power play, though, throwing a loose rebound past Huet. Campbell, though, tallied with 2:27 left in the stanza to knot the game at 2-2.
At the 5:51 mark of the second period on another San Jose man-advantage, Boyle received a backhanded cross-ice pass from Pavelski and one-timed it past Huet. Just over three minutes later, Jeremy Roenick stole the puck from a Chicago player in the Blackhawks' zone and backhanded it in the net for a 4-2 lead.
But the Blackhawks tallied three times before the end of the stanza to take the lead. Versteeg got Chicago within one at 10:53, and Barker's blast from the blue line with 2:26 left got past a crowd of players.
Just 18 seconds after Barker's goal, Campbell faked a shot and instead sent a crisp pass to Patrick Kane for a one-timer, giving Chicago the 5-4 edge.