"It's his fault," Carter said of Allen.
Allen, Carter's Olympic teammate in Sydney, challenged Carter to see who would have a higher free throw percentage this season.
Carter went 17-for-18 from the line.
"This past summer I asked him what he shot from the line, and he said 75 percent. I said I would beat him this year," Allen said. "He's shooting about 85 percent now, but I was hoping he'd shoot 50 percent today."
"They can't stop him so they have to foul him," Toronto coach Lenny Wilkens said.
Milwaukee coach George Karl said Carter got preferential treatment form the officials.
"Vince Carter is a great player but I don't think even he likes to be kissed like that," Karl said. "He could do anything and get a foul."
When told of Karl's comments, Carter said: "Wow. I don't know what to say. Tell him I'm sorry. I thought the fouls I got were legitimate."
Toronto's Charles Oakley agreed.
"He could have gotten a couple of flagrant fouls but they didn't call them," Oakley said. "Don't cry when there is no more water left. Just go buy some more and start to drink it."
Carter, who leads the NBA in scoring, had 30 points in the second half includig six in a decisive 10-0 run late in the game. He finished three points shy of his career-high.
Carter's total was the highest in the league this season. Detroit's Jerry Stackhouse had 44 against Toronto on Oct. 31
Allen guarded Carter for most of the game and scored 29 points. Carter scored 47 against Allen last season after Allen was chosen over Carter for the Olympic team. Carter was later added to the team.
"I don't think Vince can he stopped," Allen said. "When he penetrates, it doesn't matter how many bodies you get on him. Vince is hungry. What he's accomplished is great, but he has a lot more."
Allen tied the game at 98 with a jumper with just under five minutes remaining, but the Raptors went on a 10-0 run as Carter had an alley-oop jam, two free throws and a layup. Antonio Davis followed with a three-point play and a free throw to make it 108-98 with just over two minutes remaining.
Carter, who scored 37 points in Thursday's loss to Portland, finished 14-for-31 from the field and also had a season high 10 rebounds.
"This was a big win, especially after a tough loss to Portland," Carter said. "Free throws are important to me because I'm trying to improve my percentage."
Glenn Robinson had 25 for Milwaukee.
The Bucks began the second half on a 9-0 run and led by 14, but Carter scored 17 points in the third quarter as the Raptors closed within four by the start of the fourth.
"Toronto made a heck of a comeback," Milwaukee's Sam Cassell said. "Vince is going to be Vince. It's going to be a tough cover for anyone."
Carter and Allen each had 18 points at the half and Robinson and Tim Thomas each had 11 as the Bucks led 58-51.
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