Lowry had a season-high 34 points, two below his career best. He also added 11 assists and five rebounds for the Raptors, who have lost two straight and eight of nine.
Mickael Pietrus scored 21 points, DeMar DeRozan added 14 and Ed Davis chipped in 13 points and 11 rebounds.
"That's the ballgame right there: They had 56 points in the paint," Toronto coach Dwane Casey said. "They had their way with us in the paint. Everybody's going to look at Tyreke Evans. He hit two 3s and he hit six all season. We did the right thing trying to protect the paint."
After Lowry hit a 3 and followed with a shot from close range, Cousins responded with a three-point play and a jumper, tying the score at 91 with 4:31 to go. A left-handed shot off the glass by Cousins put the Kings ahead 95-93 with 2:36 left.
Pietrus made a pair of free throws early in the fourth quarter, concluding a 22-5 run that began midway through the third. But the Kings rallied quickly, taking an 85-84 lead on Jimmer Fredette's runner in the lane at the 8:09 mark.
"You can't explain in words how frustrating it is," DeRozan said. "We try to work as hard as we can, but the ball doesn't bounce our way, the ball doesn't go in when you need it to go in. It's everything you can think of."
Salmons made a pair of 3s early in the third and scored eight points as Sacramento built its lead to 73-60 midway through the period. Lowry helped bring the Raptors back, scoring 15 points in cutting the Kings' lead to 78-76 entering the fourth.
Cousins scored 14 points and Thompson had 11 in the first half, helping the Kings take a 55-47 lead.
Operating exclusively inside, the struggling Cousins got going early, scoring 12 points in the first quarter. Pietrus had 11 for Toronto, which was outscored 26-18 in the second.
NOTES: Pietrus has started two of the three games since he was signed by the Raptors as a free agent on Nov. 30. ... The Kings are 4-1 this season when they score 100 or more points. ... Former Raptor James Johnson came off the bench to start the second quarter and quickly made a 3-pointer, his first of the season after missing his first eight tries. He finished with six points, eight rebounds and five fouls in 14 minutes. ... Raptors reserve forward Linas Kleiza (sore left hip) missed his second straight game.