The ex-Valencia man was declared fit to play shortly before kick-off at Camp Nou, and is one of the senior figures as Vilanova has decided to rest many of his stars
The Spain international had been a doubt due to an ankle complaint, but passed a fitness test on the afternoon of the match and will partner Cristian Tello and Sergi Roberto in an attacking trio.
Villa is one of the few regular starters to be given a place for the Copa del Rey clash, with coach Tito Vilanova opting to rest a host of stars.
3-0 up after the first leg, Vilanova can afford to rest the likes of Lionel Messi, Xavi, Andres Iniesta, Dani Alves and Cesc Fabregas, all of whom took the field at the weekend against Levante. The latter, along with Pedro, could feature at some point after being included on the substitutes' bench.
Barcelona (4-3-3): Pinto; Montoya, Mascherano, Puyol, Adriano; Dos Santos, Thiago, Song; Tello, Villa, S. Roberto.
Alaves (5-4-1): Sergio Herrera; Oscar Rubio, Agustin, Luciano Gonzalez, Javi Hernandez, Manu García; Jaume, Miki, Jonan, Luismi; Viguera.