Harrington led Golden State (0-2) with 26 points, adding 11 rebounds. Stephen Jackson finished with 19 points. Andris Biedrins had 17 points and 13 rebounds for the Warriors.
Golden State lost 108-103 to New Orleans on Wednesday, giving up a go-ahead basket to Hornets guard Chris Paul in the final 15 seconds.
On Friday it was Bosh who denied Golden State, tying the game at 96-96 on a pair of free throws with 14.5 seconds left in regulation. The Raptors sealed it with an 10-2 run to begin the extra session, including four points from Bosh.
"Toward the end of the game, Chris Bosh just took over, playing like the All-Star he is," Jackson said. "He made plays and knocked down his free throws and there wasn't too much we could do."
Harrington said the Warriors still don't have the fitness they need to make shots late in games. Golden State shot 7-for-19 in the fourth quarter.
"In the preseason, we weren't playing 40 minutes," Harrington said. "Right now we are, so it's something we've got to get used to, get adjusted to, and quick.
"The preseason is usually a time where you're resting. It seems like we should have been playing a little bit more so we'd be prepared for now. It's going to take us a couple of games to get adjusted to and then we'll start knocking our shots down in the fourth."
Jackson, who played all 48 minutes in the season opener, ended up playing 44 on Friday, fouling out in the final minute of overtime. Jackson has taken on point duties while Monta Ellis serves a 30-game suspension after injuring his ankle in an offseason scooter accident, and said adjusting to his new role has been tough.
"This is definitely new, but I've got to speed up my learning process," Jackson said. "I don't have 30 games to learn, I've got to try to get it right now. I really take pride in putting this team on my back and being the leader of this team so I've got to play better."
Corey Maggette, who led Golden State with 27 points in Wednesday's loss to New Orleans, was held to 14, while Kelenna Azubuike came off the bench to score 15.
"We had the game, some errors at the end just killed us," Maggette said.
With the score tied after Bosh's free throws, the Warriors gave the ball to Maggette, who let the clock run down to 5 seconds, then turned it over as he drove to the basket, giving the Raptors the ball with 0.7 seconds left in regulation. Bargnani inbounded to Parker, who got a shot off, but it rimmed out, sending the game to overtime.
Parker made two of his four steals on the first two possessions of overtime, sparking an 8-0 Toronto run.
Jermaine O'Neal shot 2-for-10 and finished with five points and six rebounds, but made three blocks. O'Neal fell to the floor after blocking a second-quarter shot by Brandon Wright, wagged his finger while still on his back, then got up and said "No way" to the Golden State bench as he ran up the court.
"That was funny," Bosh said. "It was a very, very good play, but that was comical."
Toronto led 51-50 at the half.
Golden State picked up the third-year options on guard Marco Belinelli and Wright, and declined the fourth-year option on guard Marcus Williams. ... Each of Toronto's first five baskets was scored by a different member of the starting lineup. ... Bosh delivered a brief pre-game address to fans, thanking them for their support.