It was Boca who created the first chance when Cristian Pavon stole possession in the halfway line to play in Lucas Olaza who then whipped in a cross for Pablo Perez at the back post to hit the target, but the ball went wide.
It was all nervy at the start, with neither side too keen to seize initiative to get on the front-foot and to not make a mistake.
A poor strike from Dario Benedetto strike came out poor but deflected off the River wall to cause havoc and drop kindly for Perez, who pings an effort goalwards but it was blocked before looping up into the air.
Boca went close, but Francesco Armani did brilliantly to claw the ball away from Benedetto with a brave, two-handed save.
Boca countered upfield superbly, and Benedetto applied composure to finish beyond Armani a minute to the break.
River was all over the show five minutes into the second half, with Lucas Pratto the main instigator in attack.
The striker appealed for a penalty after being nugged down, but it was quickly waved away by the match officials.
Boca drew level when Pratto showed great instincts to guide him an assist by Gonzalo Martinez on 61 minutes.
River were shocked and were dumbfounded of ideas going forward, with Boca seizing forward but lacked the killer touch as the game headed to extra time in Madrid.
Following a fast-paced opening, Boca were dealt a blow. Wilmar Barrios was given a straight red card for a horrific studs up challenge on Wilson Palacios.
18-year-old Julian Alvarez aimed to steal the show for the visitors, but flashed his effort narrowly wide of target.
Inside a minute, Martinez found space at the back post but volleyed harmlessly over the post.
In the second phase, River regained the lead when Juan Fernando Quintero slid in from the right to find the bottom corner exquisitely.
Veteran Carlos Tevez was finally brought on after a lenghty warm-up on the touchline.
River repelled with a couple of corners, but good goalkeeping from Armani kept them from extending their tally.
Armani made arguably a game-changing save from a powerful shot from 30-metres by Fernando Gago.
River was almost in for a third, but the post came to the rescue of River following a shot from Leonardo Jara.
The third did came and Martinez made sure of the title when he finished off a move on the counterattack to hand River the title of South American kings 2018.