Kristaps Porzingis had 25 points and eight rebounds as the Mavericks played their third consecutive game without star Luka Doncic because of a sprained left knee and ankle.
Jalen Brunson scored 20 points for the Mavericks, who have lost all three games without Doncic to open a four-game road trip.
"I thought we had a lot of great looks at 3 that were just short tonight for whatever reason," Mavericks coach Jason Kidd said of his team that was just 20% (6 of 30) from 3-point range.
"In that fourth quarter, when things weren't going well, I thought we improved to give ourselves a chance to win on the road."
The Mavericks led by as many as nine points in a rough-shooting first half in which both teams shot under 42% from the field. The Clippers rallied to pull within 47-46 at halftime.
The Clippers shot 55.6% (10 of 18) in the third quarter, getting half of their made shots from 3-point range while taking a 71-62 lead.
The Mavericks pulled within 78-75 on Tim Hardaway Jr.‘s 3-pointer with 7:33 remaining before the Clippers went on a 9-0 run for an 87-75 lead.
"It's been a process, honestly," Jackson said. "There are games when we play well and there are games where we hit these lulls and are still trying to figure each other out. … I think we all just found easier shots today."
The Mavericks appeared to pull within 94-91 with 52 seconds remaining after a basket by Brunson, but a foul on the Clippers' Terance Mann was rescinded and the basket was taken away. Jackson then scored inside to give the Clippers a 96-89 lead with 29 seconds to play.
"I thought he got fouled and made a great play," Kidd said. "It's a strange play because we lose the two points and then we lose the ball. It puts you in a difficult situation coming down the stretch."
Ivica Zubac had 16 points and 10 rebounds for the Clippers in the opener of a six-game home stretch.
The teams were meeting for the first time since the Clippers staved off elimination in the first round of last season's playoffs by winning Game 6 and 7 to advance.
Mavericks: Doncic went through pregame shooting drills but was ruled out on a game-time decision. … After missing nine consecutive games with a left oblique strain, F Maxi Kleber returned to score five points in 20 minutes. … G Frank Ntilikina (three points on 1-of-6 shooting) left after nine minutes and did not play in the second half because of a right calf injury.
Clippers: C Serge Ibaka was activated for the first time since Nov. 9 and for just the third time this season after a G League stint to get him up to speed after offseason back surgery. He scored six points in 12 minutes. … G Amir Coffey made his second start in three games and just the fourth of his career.
Mavericks: Play at the Clippers on Tuesday.