O'Neal, preparing for his first season with the Raptors after eight years with Indiana and four with Portland, finished 7-for-15 from the field in 33 minutes and grabbed nine rebounds. Bosh had 11 boards.
Reserve Ricky Davis led the Clippers (3-1) with 14 points. First-round draft pick Eric Gordon, the third player off the bench, had 10 points in 18 minutes after scoring 33 points in Wednesday's victory over Sacramento.
Gordon finished with a rush, making a layup and a pair of 3-pointers 27 seconds apart to slice a 13-point deficit to 91-86 with 43 seconds to play. But he missed a rushed 3-point shot off a tipped ball, and Roko Ukic hit a pair of free throws for Toronto with 10 seconds left to help seal the victory. Ukic scored all of his eight points in the final quarter.
Clippers coach Mike Dunleavy, whose players were sidelined for a combined 321 games last season due to injuries that forced him to use 39 different starting lineups, finds himself scrambling again for healthy players. Tim Thomas sat out because of a groin strain. Oft-injured Marcus Camby couldn't play because of a bruised heel.
Point guard Baron Davis, who missed the previous two games because of the flu, sprained the ring finger on his left hand at practice Friday and will miss Sunday's game as well. X-rays did not reveal a break, and an MRI was inconclusive, so Davis will be examined by a hand specialist on Sunday.
Dunleavy said before the game that all three players should be ready for the season opener against the Lakers on Oct. 29.
Neither team led by more than five points until Bosh hit a 3-pointer that extended Toronto's lead to 60-52 with 8:34 left in the third quarter. All five Clippers starters -- and Davis -- had double digits through three, but Bosh and O'Neal trumped that balanced scoring attack with their two-man show.
Bosh and O'Neal combined for 30 points in the first half to help the Raptors (4-2) take a 53-52 lead. Forward Andrea Bargnani, who led Toronto with a 14.6 scoring average through the first five games, did not play because of a bruised right leg.
One of the referees working the game was Haywoode Workman, who played guard for five teams during his 10 NBA seasons and ended his pro career with the Raptors in 1999-00. The 42-year-old North Carolina native is one of three referees in NBA history to also have played in the league, along with Bernie Fryer and Leon Wood.