Barcelona seals quarterfinals ticket
The Spain striker has struggled to find minutes since returning from a broken leg. But he again proved he hasn't lost his scoring touch with two fine goals to follow Thiago Alcantara's opener at Camp Nou stadium.
Barcelona eased by its second-division opponent 7-0 on aggregate after Alexis Sanchez added two goals in the second half.
Villa's quest to regain his prominent role in Barcelona's attack may have suffered another blow, however, when he retired late after apparently pulling a muscle in his right thigh.
Barcelona now faces three games in the next two weeks against Malaga. The two teams play on Sunday in the Spanish league and then twice more in the Copa.
Atletico Madrid will meet Real Betis in another quarterfinal after they both wrapped up their last-16 ties on Thursday.
Barcelona star Lionel Messi, who was awarded his fourth straight Ballon d'Or on Monday, never left the bench. He had already scored Barcelona's two goals in the first leg.
Barcelona also rested first-choice midfielders Xavi Hernandez and Andres Iniesta while Sergio Busquets was reserved as a substitute.
Thiago opened for the hosts in the 17th minute when he ran onto Alex Song's chipped pass and slotted a right-footed shot past goalkeeper Mikel Saizar.
Villa doubled the lead four minutes later with a beautiful slalom down the left flank to dribble by a defender before he gently lofted the ball over the onrushing Saizar. He netted again in the 26th with a hard blast that hit the far post before nestling into the back of the net.
Despite not enjoying much playing time this season, Villa has scored 10 goals in all competitions.
Alexis, who had missed two clear chances in front of an open net, headed in a corner kick in the 55th and tapped in his second in the 85th. The Chile forward had only scored one goal previously this campaign.
Villa appeared to hurt his right thigh after a sprint and had to go off after trying to continue, leaving Barcelona with 10 men for the final 13 minutes having made all there substitutes.
They are joined in the quarterfinals by Atletico Madrid and Real Betis, although the latter only just saw off Las Palmas with Ruben Castro's 85th-minute goal giving them a 1-0 win on the night, 2-1 on aggregate.
Las Palmas had Enrique Corrales sent off in the final minute for a second bookable offence.
Getafe held Atletico to a 0-0 draw on the night but, after Rafa Lopez's 33rd-minute dismissal, had little hope of overturning a 3-0 deficit from the first leg.