Jones broke out of a tie with Laura Diaz, who had birdied the 18th to move to 11-under 272. After driving into the rough on 18, Jones got up and down on her third shot to set up a birdie putt for her second win this year and 12th overall.
The 42-year-old had a three-shot lead heading into the final round, but the lead fell to two after she three-putted the par-3 16th.
'I was nervous with the putter all day,' said Jones, who picked up $142,500. 'So if I was going to lose a tournament, I would think it's probably with the putter. And these greens here are tough. You never have something straight up or straight down.'
Despite her putting woes, Jones was able to sink the birdie putt on 18 and avoid a playoff. Her win at the Big Apple Classic adds to her collection of victories in the empire state.
'New York, New York, I tell you, I've won five tournaments in New York. I've won 12 tournaments, five of them are in New York.'
Jones had come close to winning this event in the past, including second place finishes in 1993 and 2000.
'It gives me a good history at this golf course. I've had a lot of fun in this tournament,' she said. 'I don't like going home in second place, especially two years in a row, but the chase is great.'
Her 12-under total matched the second lowest score in the history of this event.
Diaz responded from a bogey on 17 to make birdie on 18 in search of her first win of the year, but after Jones's birdie settled for her fourth second-place finish in 2001.
'I knew that put me to 11 [under], and I knew that had to have been pretty good because of the feedback from the gallery,' she said. 'And then I looked at the board. But, you know, I mean, 18 is a hole that a lot of people make birdie on; Rosie did it.'
Kris Tschetter ended the round three strokes off the lead at 10-under 274 for her third consecutive top-10 finish.
Full-field scores from the Big Apple Classic