"We'll take any victory," Boozer said. "It wasn't pretty, but they did a good job defensively and we did a good job defensively. On offense we struggled but we came out with a big victory."
Mehmet Okur scored 13 points and Ronnie Brewer added 12 for the Jazz in a sloppy affair that saw the teams combine for 32 turnovers.
"I don't think we played good tonight but we won the game," Okur said. "On the road, I'll take that."
A 3-pointer by T.J. Ford brought Toronto to 89-88 with 18 seconds remaining. Toronto fouled Williams, who made both free throws and, after Ford's 3-point attempt bounced off the rim, Boozer made a free throw to seal the win.
Ford and Jason Kapono both missed 3-pointers for Toronto in the final 6.9 seconds.
Utah (7-2) won despite failing to top 100 points for just the second time this season. The Jazz entered play Wednesday as the league's highest-scoring team, averaging 111.9 points.
The Jazz came in shooting 50 percent as a team, but were held to 43 percent by the Raptors. Like Boozer, Williams credited Toronto's defense for keeping the score low.
"We were just missing shots, we weren't as crisp as we usually are offensively," Williams said. "A lot of it has to do with their defense. They're a solid defensive team. They pressure you, they make you work."
While he doesn't expect the Jazz to consistently score more than 100 points, Boozer said the key is persistence.
"You've just got to keep playing," Boozer said. "You can't go through 82 games in perfect harmony. Some games are going to be difficult and today was definitely difficult. They did a good job of getting to us, we did a good job of getting to them, obviously, and we did enough to win."
Utah's Andrei Kirilenko finished with eight points, nine rebounds, 11 assists and five steals.
"I can't say enough about AK right now," Boozer said. "He's scoring, rebounding, getting assists, getting steals. He's everywhere. Even if he's not scoring, you know he's doing other stuff that helps us win."
Anthony Parker led Toronto with 19 points, while rookie Jamario Moon, making just his second career start, scored a career-high 15. Chris Bosh had 14 points and seven rebounds for Toronto (4-4), which dropped to 1-3 at home.
"We just have to keep shooting, keep shooting, keep shooting," Bosh said. "Eventually we want to get on a roll at home and do a better job of protecting our home court."
Ford finished with 13 points and eight assists.
Toronto's Andrea Bargnani scored only two points and made just one of his 11 field goal attempts.
Toronto's Rasho Nesterovic left the game midway through the third quarter after spraining his right ankle when he landed on Okur's foot on a rebound. He did not return.
Jazz coach Jerry Sloan called time with 3:43 left in the third with the Raptors leading 57-54. Utah responded with an 8-0 run and outscored Toronto 10-2 the rest of the period, taking a 64-59 edge into the final 12 minutes.
Utah led 39-36 at the half.
Utah's Matt Harpring missed the game because of a flu-like virus. Rookie forward Morris Almond took Harpring's place on the roster. ... Toronto FC head coach Mo Johnston watched the game from courtside seats.