The keeper, on loan from Juventus, headed in Danilo Cataldi’s free-kick to end a record-breaking run of 14 defeats.
Milan led through Giacomo Bonaventura before George Puscas equalised.
Nikola Kalinic headed Milan ahead again and they had Alessio Romagnoli sent off before Brignoli’s late leveller.
“I’m not just happy for me but for everyone,” Brignoli said. “We’ve lost so many games undeservedly with goals in the 90th minute but now it’s our turn to celebrate.
“It’s a dream to be in Serie A although we hoped that it would have turned out better than this. There was nothing to lose. I just closed my eyes and jumped. It was a goalkeeper’s goal, not a forward’s goal.”
Milan, who drop to eight, sacked manager Vincenzo Montella earlier this week andreplaced him with youth-team boss Gennaro Gattuso.
“It hurts. A knife wound would have been less painful than that goal. I would never have expected to concede a goal in the last minute with the opposition goalkeeper scoring,” the new manager said.
Serie A debutants Benevento – who were in the third tier in 2015-16 – had lost more games at the start of a season than any team in history from Europe’s top five leagues.
Brignoli is the first goalkeeper to score in Serie A since Massimo Taibi for Reggina against Udinese in 2001.