The left-back outleaped the entire Boca defence to meet a corner in the dying minutes of the game, steering the ball into the net to give his side a decisive advantage.
Heavy rain throughout the day meant the pitch at Boca's Bombonera home was in a slippery state, and that dampness took its toll on play. Plenty of falls and misplaced passes made for a scrappy match between the two Buenos Aires giants.
A wonderful goal from River Plate youngster Manuel Lanzini gave the visitors the lead over Boca Juniors just after half time, after a first 45 minutes made difficult by adverse weather conditions.
The No. 10 broke through the Boca back-line just before the hour mark to latch on to Teo Gutiérrez's pass, and finished with a delicate chip over goalkeeper Agustín Orión opening up a game that had threatened to go either way previously.
Boca Juniors veteran Juan Román Riquelme had previously come up with a special effort from a dead-ball situation to bring the Xeneize back into the Superclásico, after the hosts had fallen behind to River Plate.
An impeccably placed free kick from the ex-Barcelona and Villarreal man left the derby poised at 1-1 with just over 20 minutes to play, after River struck first in Argentina's biggest football match of the year.
But Funes Mori was on hand to give River the victory they had awaited for so long, in turn sending Ramón Díaz's team joint-second in the Final tournament.
Boca, meanwhile, stay in 12th position with just 12 points from the year so far, heaping further pressure on coach Carlos Bianchi.
