Reserve Toney Douglas added 19 points and Landry Fields had 14, making three big 3-pointers in the fourth quarter as the Knicks won for just the second time in six games and improved to 27-26.
Stoudemire missed his first game of the season with a sprained right big toe, but the Knicks overcame their All-Star's absence by making 16 3-pointers, including Chandler's that gave them the lead for good with 4:08 left.
New York hasn't had a losing record since falling to 8-9 after a loss to Atlanta on Nov. 27. The Knicks were 22-15 on Jan. 11 but have stumbled since, with Stoudemire and fellow captain Raymond Felton hinting after Friday's loss to the Los Angeles Lakers that the Carmelo Anthony trade speculation was partially behind their slump.
Devin Harris scored 22 for the Nets, who were bidding for their first three-game winning streak in two years. Brook Lopez added 19 and Sasha Vujacic chipped in 15, but New Jersey shot just 42 percent from the field.
The game drew an announced crowd of 18,711, the Nets' first sellout of the season in their temporary home at the Prudential Center. But it was a pro-Knicks crowd that cheered louder for the visitors as they took control in the closing minutes.
Vujacic's 3-pointer tied it at 72 in the opening minute of the fourth quarter, but the Knicks answered with 3s by Fields, Bill Walker and Douglas in an 11-2 spurt for an 83-74 lead. New Jersey came right back with 10 in a row, going ahead 84-83 on Harris' 3-pointer with 7:02 to go.
It was back and forth from there until Chandler and Fields hit consecutive 3-pointers for a 93-89 edge with 2:52 remaining. Lopez made a free throw before Timofey Mozgov converted a three-point play, and Fields followed a free throw by Harris with another 3 from the corner to put it away at 99-91 with 48 seconds to go.
Stoudemire's absence was announced about 45 minutes before the game, with a Knicks official saying their leading scorer wasn't sure how he was hurt. Stoudemire played 32 minutes Friday in a 113-96 loss to the Lakers, finishing with 24 points and 10 rebounds.
Without him, the Knicks relied on their 3-point shooting and a solid defensive effort to lead for much of the first half. They hit eight of their first 13 behind the arc, and used an 8-2 burst midway through the second quarter to open a 44-33 lead on Douglas' layup.
Chandler had 12 points and Douglas 11 off the bench as the Knicks led 59-54 at the half, holding the Nets to 43 percent shooting.
The teams combined for just 11 baskets and 27 points in a miserable third quarter. The Knicks were 1 of 10 behind the arc in the period, but the Nets could only take one point off their halftime deficit, with New York taking a 72-68 advantage to the fourth after Douglas' 3-pointer with 21 seconds left.
Notes: The Nets last won three in a row during a four-game winning streak from Jan. 31-Feb. 7, 2009. ... Ronny Turiaf played for the Knicks after missing the last three games with a sprained right ankle. ... The Nets lead the series 81-80. ... Despite the teams' proximity, Avery Johnson said there is no rivalry until the teams consistently make and occasionally meet in the playoffs. But what about when the Nets move to Brooklyn in 2012? "I don't know. We'll cross that bridge when we get there," Johnson said.