Second half goals from the 28-year-old forward and Cheryshev gave Fran Escribá’s men a fine start in the Group A of the European tournament, after suffering a 3-0 defeat to Real Sociedad on Sunday.
Nicola Sansone broke the deadlock in the 16th minute to give the home fans something to cheer on before referee Sran Jovanović blew the whistle for half-time.
After the restart, Yuri Logvinenko got the Kazakhstan league champions back into the game with an equaliser in the 68th minute.
His introduction for Sansone two minutes later, made a difference for the La Liga side as the DR Congo international made a brilliant run towards goal and fired the Yellow Submarines ahead again with a fine finish in the 75th minute.
Denis Cheryshev who replaced Pablo Fornals in the 74th minute wrap up the win with his strike in the 77th minute.
Villarreal sit atop of the Group A standings and will visit Maccabi Tel Aviv for their next Europa League outing on September 28.