Jennifer reportedly wasn't pleased with Chris' chummy friendship with ex-wife Gwyneth, 42 - the two share daughter Apple, nine, and son Moses, seven.
But an insider told the magazine that the Silver Linings Playbook star has come terms with the situation now.
"Jennifer understands that the children come first with Chris and that his relationship with Gwyneth is based around the family and will always be a part of his life," the insider told People.
"Things are good between them," added the insider.
During their cosy meal at Kiwami sushi restaurant, the pair seemed to have eyes only for each other and 'were engulfed in their little world of conversation,' according to People.
Jennifer, who used chopsticks, was dressed casually in a grey blazer over a black ensemble, and her blonde hair fell on either side of her face in straight bands.
The Coldplay singer looked comfortable too while showing off thick stubble as he listened intently to what Jennifer was saying.
And as long as they have cell phones, communication shouldn't be problem. Jennifer, who jetted out of Los Angeles on Monday, was spotted arriving to her hotel in snowy New York City with a phone pressed to her ear beneath a baseball cap.
She was dressed in clingy athletic leggings, high-top trainers, white top and a black bomber jacket featuring faux fur trim.
Meanwhile, as news of Jennifer and Chris' rekindled romance emerged, so did Gwyneth's British Harper's Bazaar interview in which she admitted she's had doubts about letting Martin go.
"Of course, there are times when I think it would have been better if we had stayed married, which is always what your children want," she said. "But we have been able to solidify this friendship, so that we're really close."
- Daily Mail