Despite being under large amounts of pressure and behind for much of the game the Uruguayan striker netted a close-range finish in the dying moments to put the visitors through
The Argentines found themselves under immense pressure throughout but after Thiago Carleto levelled the tie early on, the game grew stale with neither team willing to commit too much. With the game dangerously poised the final blow came in stoppage time as Santiago Silva slotted home a vital goal that saw the visitors progress 2-1 on aggregate.
Knowing that they needed to win the match, Flu enjoyed a lot of possession in the early stages. With Boca chasing the ball the visitors gave away a free kick in the centre of the field, 30 yards from goal. Carleto stepped up to strike the ball and arrowed his effort straight into the wall but a wicked deflection saw it sneak in at the bottom corner past a scrambling Agustin Orion.
Fluzao's midfield were indomitable as the hosts played with a high level of intensity and began to win the majority of the battles in midfield. But for all they saw of the ball, goal scoring opportunities proved hard to come by and a left-footed curler from Thiago Neves which forced the keeper into a rare save was their only other shot at goal.
Having struggled to get involved in the first half, Julio Cesar Falcioni's men improved vastly after the break. They pressed high and earned themselves a number of corners from which Rolando Schiavi looked threatening but failed to test Diego Cavalieri.
Carleto frequently provided Flu with a man over on the left and they used this to regain control of the game and their next gilt-edged chance came on the hour mark. Thiago Neves drilled in a low cross from the left which was met by Rafael Sobis inside the six-yard box but the striker's contact was too weak and he failed to direct the ball on target.
With the tie level and thus heading to penalties Boca were the first team to make an attacking move as Pablo Mouche replaced the ineffectual Dario Cvitanich with just over 20 minutes remaining. Abel Braga reacted by sending on Wellington Nem in place of Wagner in attempt to win the tie in regulation time.
Neither player managed to have the required impact but the game was to be decided in stoppage time. A swift break from the visitors enabled Diego Rivero to break into right-hand side of the box. His shot hit the post and Diego Cavalieri instincitvely got a hand to the ball. Unfortunately for the keeper he played the ball straight to Santiago Silva who tapped in the rebound.
Boca will now face the winner of the Universidad de Chile and Libertad tie unless Velez Sarsfield eliminate Santos, then the two Argentine teams would be forced to play each other.