The Basque club overturned last week's 2-1 loss in the Portuguese capital, with a late goal from the Spain striker securing the victoryAthletic Bilbao booked its place in the Europa League final against Atletico Madrid with a 3-1 victory over Sporting Lisbon at San Mames.
The Portuguese side had claimed a 2-1 victory in Lisbon a week ago, but goals from Markel Susaeta, Ibai Gomez and Fernando Llorente were enough to see Marcelo Bielsa's to progess, despite a Ricky Van Wolfswinkel goal.
It was the Portuguese side which came out of the blocks quicker. A poorly cleared Matias Fernandez corner fell to Anderson Polga, who could only head the ball straight at Gorka Iraizoz when he should have done better.
Soon after, the Chilean sent a free kick well over, from distance, but it was not long before the hosts sprung into action.
Fernando Llorente brought the ball down well seconds after Fernandez's free kick, but when he finally wriggled free of Xandao, he failed to send a meaningful shot in.
Marcelo Bielsa's side was starting to apply heavy pressure. Some fantastic footwork from Gomez fooled the Sporting backline, but the 22-year-old could only fire a shot straight at Rui Patricio.
Soon, however, the breakthrough arrived. Llorente padded an Iker Muniain cross straight to Susaeta, who volleyed past Patricio to put his side in front.
The Bilbao goal would have seen the hosts go through on away goals, but Sporting soon set about in pursuit of an equalizer.
Diego Capel, the hero of the first leg, sent a deep cross to the far post, but Andre Martin could only send a header wide when he should have done far better.
Soon afterwards, Iraizoz was called into action to palm away an Polga header after the Brazilian found himself on the end of Capel's corner.
Throughout Sporting's period of pressure, Athletic continued to fashion chances. Gomez had a header rightly ruled out for offside, before Llorente squeezed a volley goal-wards, forcing Patricio to palm the ball away with his fingertips.
The equalizer finally came just before the break, though. Another corner proved to be the cause of confusion in the Bilbao defence, and Van Wolfswinkel capitalized by sending a left-footed volley into the bottom corner.
However, the Dutchman's effort was not enough to ensure parity at the break. Llorente held up the ball fantastically once again, and slipped in Gomez, who slipped it past Patricio to level the tie.
At the other end, the woodwork soon turned into Athletic's savior. Emiliano Insua belted a ferocious free kick goal-wards, and a heavy deflection took the ball past Iraizoz, but onto the post.
Soon, though, the match settled into a more steady rhythm. Muniain forced a decent save from Patricio with a tame header, before the Portuguese 'keeper had Insua to thank when he dropped an Ibai free kick, only for the Argentine to remove the danger, hacking the ball off the line.
Finally, the Portuguese resistance was broken with just minutes remaining. Gomez sent a low ball across the face of goal, and Llorente stuck out a leg to prod the ball into the net, via the post.
In the wake of the goal, Sporting sent the ball long in an effort to steal a place in the final, but it was to no avail: it was Bilbao's night.