"We shouldn't have lost this one," Ginobili said. "It's important to go into the break feeling good about yourself and on a good stretch. We were playing a team that isn't doing so well and has two injured players, so we should have done much better."
Toronto forward Chris Bosh missed his fourth straight game with a sprained right knee, and point guard Jose Calderon sat out with a sore right hamstring.
The Raptors were reduced to nine available players when forward Joey Graham, who tied a career high with 24 points in Tuesday's win at Minnesota, left with 2:56 remaining in the first because of a bruised right shin.
Tim Duncan had 20 points and 13 rebounds and Tony Parker added 22 points for San Antonio, but missed what would have been a tying jumper at the buzzer.
"We had a couple of different options but they played good D on it and it didn't work out," Spurs coach Gregg Popovich said of Parker's last-second miss.
Ginobili scored 15 in the fourth quarter and matched his season high, but it wasn't enough for the Spurs, who had won 11 of 13 coming in.
"It's a really tough one," Ginobili said. "We didn't have a good game. For most of the game we were in control but down the stretch we just couldn't score anymore and they made some great plays."
Ukic, a rookie, made two of the biggest for Toronto, following his 3-pointer from the corner with a running jumper in the lane to put Toronto up 90-89 with 20.8 seconds left.
"I really like those situations when I have the ball on top and I just think of scoring," Ukic said of his go-ahead basket. "I feel pretty comfortable in this situation. I didn't feel much pressure, I saw the lane was pretty much open and I just tried to go all the way to the basket."
"He's a confident kid," Kapono said. "He's been playing pro since he was 6 years old. He's been collecting a check for 20 years now. His experience is vast."
Spurs guard Roger Mason said Ukic likely felt more comfortable knowing Calderon wasn't available to replace him.
"For a rookie point guard, he took some big shots and made some big shots," Mason said. "It's like that sometimes when guys are injured and you don't look over your shoulder, you just go out and leave it out there. I think his confidence improved every shot he made and he hit the biggest shot of the game."
Kapono scored 21 as the Raptors won for just the second time in eight games.
"We played extremely well as a team," Kapono said. "We were down, in terms of guys, and everyone stepped up."
Trailing 69-67 after three quarters, Toronto stayed close despite missing eight of 10 shots to begin the fourth. Anthony Parker and Ukic each made 3-pointers on either side of two Tony Parker free throws to make it 89-88 with 49 seconds left.
Toronto got the ball back after Tony Parker's miss and Ukic gave Toronto the lead with a running jumper over the Spurs' Parker.
Ginobili missed a driving shot at the other end and Toronto's Jermaine O'Neal grabbed his 10th rebound. O'Neal was fouled and made one of two free throws, giving San Antonio one final chance with 6.3 seconds remaining. But Tony Parker's final shot fell short after a broken play by the Spurs.
"We wanted Manu on the backdoor and Tim to go one-on-one," Parker said. "Tim saw [Michael Finley] wide open and I thought Fin was going to take the 3. Then, when he passed it to me, there was like three seconds left, so I tried to do whatever I could."
Duncan scored 10 points and Tony Parker had eight to give the Spurs a 22-20 lead after the first quarter.
Kapono and Ukic each had eight points in the second, with Ukic shooting 4-for-4, as Toronto took a 49-43 edge at the half.
San Antonio's Matt Bonner, who spent the first two years of his career with the Raptors, is in the process of becoming a Canadian citizen and hopes to play for Canada's national team. Born in New Hampshire, Bonner has a grandfather from Newfoundland and his wife is from Toronto. "I feel very strongly about representing Canada," Bonner said. "I feel like I'm part Canadian. It just feels right." ... Toronto forward Kris Humphries has been out since Jan. 18 with a broken right leg.