Major League Soccer's most valuable player of the year, Barros Schelotto masterminded a spirited display by the Crew after they survived an early onslaught from New York at the Home Depot Center.
The 35-year-old former Boca Juniors favourite set up Venezuelan forward Alejandro Moreno for the first goal in the 31st minute before creating openings for second-half strikes by Chad Marshall and Frankie Hejduk.
New York, unfortunate not to score before halftime, had equalised through forward John Wolyniec in the 51st minute.
"I'm still a little bit numb, you go through a number of emotions when you win a game like this," Columbus coach Sigi Schmid told reporters after his team's first MLS Cup triumph. "I'm just very proud of what our team did all season."
Columbus ended the MLS regular season with a league best record of 17-7-6 and 57 points.
"We found different ways to win at various times and the individual play of this guy next to me was tremendous," Schmid added, looking at Barros Schelotto who was voted the MLS Cup's most valuable player."
A 27,000 crowd watched in bright sunshine as the Red Bulls dominated the early exchanges, with Dutchman Dave van den Bergh a continual threat down the left.
Van den Burgh set up defender Kevin Goldthwaite after 19 minutes but he glanced his header wide and in the 28th he found the unmarked Dane Richards whose shot flew over the bar.
Columbus opened the scoring against the run of play just after the half-hour mark when Barros Schelotto put the bearded Moreno through on the right.
DESPERATE DIVE
Moreno weaved past Columbus defender Diego Jimenez on the edge of the penalty area before threading a shot under goalkeeper Danny Cepero's dive.
The game came alive shortly after the break with two goals in two minutes.
Wolyniec levelled for New York in the 51st after being set up by Richards' darting run but Columbus regained the lead when defender Marshall headed home Barros Schelotto's corner.
The Argentine came agonisingly close to scoring himself in the 77th minute after a superb pass from Moreno but his shot struck the woodwork.
Five minutes later, Barros Schelotto was the architect of the Crew's third goal with a delicate chip over the Red Bull defense that gave United States World Cup veteran Hejduk the chance to score with a spectacular diving header.
"We were hard done in the first half when I think we were the better team with the better chances," said Red Bulls coach Juan Carlos Osorio. "But credit to the winning team and congratulations to them."
