Nowitzki, the NBA's fourth-leading scorer, was 3-of-13 from the floor and scored 10 points, just two more than his season low.
Knicks center Eddy Curry, who missed the first 33 games with a knee injury, saw his first action of the season. He entered with 2:42 left in the first quarter and scored on a layup just more than a minute later.
That's was Curry's only shot attempt in 2½ minutes of action. He also grabbed two rebounds.
Antoine Wright had 13 points, Brandon Bass added 12 and Jason Terry 10 for the Mavericks.
Chris Duhon hit his first nine shots and scored 24 points, and Wilson Chandler added 20 for the Knicks, who have lost two in a row since beating defending champion Boston on Sunday.
New York's David Lee had 13 points and 15 rebounds - his seventh consecutive double-double. Duhon finished 10-of-14 from the field.
Kidd's jumper gave the Mavericks the lead for good, 87-86 with 5:45 left. The point guard then added a 3-pointer to put Dallas up 93-89.
Al Harrington converted a three-point play to cut Dallas' lead to 95-94. The Knicks had a chance to take the lead on their next three possessions, but failed on those chances.
Nowitzki hit two free throws to put Dallas ahead by three, and Terry sealed it by hitting a long jumper with 9 seconds left.
The Knicks (6-of-24) shot 25 percent in the fourth. Over the last 2:18, they missed all six of their shots.
The Mavericks closed the third on a 10-0 run to take an 80-78 lead, their first since early in the second quarter.
Tim Thomas hit a 3-pointer to put the Knicks up 78-70. In a scoreless final 3:26 of the third, New York missed all five of its shots and turned the ball over three times.
Duhon, 9-of-9 from the floor in the first half, had 22 points as the Knicks led 59-54 at halftime.
The point guard capped his perfect half with a layup and his fourth 3-pointer of the game to give New York an eight-point edge just before halftime.
Duhon's first miss came when Erick Dampier blocked his layup attempt with 8:40 left in the third.
New York went on a 14-2 run, capped Thomas' layup, to take a 27-16 lead. Dallas cut it to 29-27 at the end of the first quarter on Jose Barea's 3-pointer.
Notes: Knicks G Nate Robinson, 1-for-9 from 3-point range Thursday, is 3-of-30 from long distance in his past five games. ...
The Mavericks have won 12 of their last 14 home games. ... Knicks coach Mike D'Antoni received a technical for arguing a foul call with 10:56 left.