The Bianconeri were in crisis after just two points from four rounds and it looked to be another bad day at the Allianz Juventus Stadium when Frosinone took a 2-1 lead again through Walid Cheddira and Marco Brescianini before half-time.
Dusan Vlahovic completed his brace to make it 2-2, but Daniele Rugani pounced from a tight angle following a corner the 95th minute to secure a precious victory.
His total came to 1,002 "real points" – so two for a win before the 1994-95 season went to three – thanks to 301 wins, 99 draws and 96 defeats.
In 496 Serie A games, Allegri averaged 2.02 points per game against Cagliari, Milan and Juventus.
He won six Serie A titles, five in a row with Juve from 2014-15 to 2018-19, and the first with Milan in 2010-11.