Nowitzki scored 11 of a game-high 28 points in the final four-and-a-half minutes of a fourth quarter that was highlighted by two dramatic swings of momentum as the Mavericks held off a furious fightback from the visiting Knicks.
In the previous meeting between the teams on February 19, Jeremy Lin tallied 28 points and 14 assists to lead New York past Dallas during the height of Lin's rapid rise to league-wide popularity.
The Mavericks (23-17) wasted little time in the rematch as they took a 27-15 lead after the first quarter and were ahead by 14 entering the fourth.
The Knicks woke from their slumber to start the final quarter with a 15-0 run that gave them an 78-77 lead with five minutes left, but the home team respond with 14 straight points to regain control and seal the victory.
"In this season, no lead is safe, no deficit is too large," Mavs coach Rick Carlisle said. "They made a heck of a run to take the lead. We made a heck of a run to put the game away."
Amar'e Stoudemire had 26 points for the Knicks (18-20), losers of two straight, while Lin added 14 but made just 4-of-13 shots to continue his recent shooting struggles.
Lin has shot just 27 percent over his last three road games, all losses. He did not receive much support from All-Star team mate Carmelo Anthony, who managed only six points on 2-for-12 shooting.
Tyson Chandler, who joined New York in the off-season, received his NBA championship ring before the game for his role in Dallas' title run last year.
The Mavericks moved into solo sixth-place in the West with their latest win, aided by 18 points off the bench from Rodrigue Beaubois.
The Knicks, meanwhile, are still clinging to the eighth and final playoff spot in the East.