The pass was intercepted by safety Robert Lester, but officials threw a flag after it appeared linebacker Luke Kuechly had interfered with tight end Rob Gronkowski by grabbing him with both hands. The officials quickly gathered together and waved off the flag.
"There was no explanation given to me. Officials ran off the field. I didn't see anything," Patriots coach Bill Belichick said. "It was the last play of the game. There was a flag thrown and then the game was over."
An angry Brady sprinted over to two officials to argue the call as they walked off the field.
"He was kind of weaving in and out of there. I didn't really want to throw it over his head and out of bounds, so I was a little indecisive," Brady said. "It wasn't a great throw. No excuses. Should have been a better throw."
Meanwhile, the Panthers celebrated.
"We had good pressure and our safety Robert Lester was in good position to make the play," coach Ron Rivera said.
Brady was 29 of 40 for 296 yards and one touchdown.
Newton completed 19 of 28 passes for 209 yards and three touchdowns. He also ran seven times for 62 yards in what will go down as one of his best games as a pro.
After the game, Rivera called it a "gutsy effort."
"It wasn't our best defensive effort, but it was one of our better offensive efforts," Rivera said. "It was good for our guys to win a game like this."
Carolina's win came eight days after a 10-9 victory over reigning NFC champion San Francisco.
Newton gave Carolina a 17-10 lead in the third quarter on an 81-yard touchdown drive that took more than 8 minutes off the clock.
Storylines Carolina wins sixth straight
R Ted Ginn Jr. scores on a 25-yard reception with 59 second remaining to give the Panthers the lead.
• Tom Brady's pass to Rob Gronkowski falls incomplete on the final play, and the officials pick up a flag instead of calling pass interference