Former Spain midfielder Pablo Hernandez had a hand in three of Valencia's goals at the Mestalla to help give the 2008 winners a healthy advantage ahead of next week's second leg at Levante's Ciutat de Valencia home.
Jonas ran on to an Hernandez pass and fired under goalkeeper Keylor Navas to give the home side a 24th-minute lead before Roberto Soldado struck in the 31st after the Levante defence failed to deal with Hernandez's cross.
"We had a few counter-attacks at the end that we could have exploited better but I think that last goal gives us a lot of breathing space for the return leg," Soldado said in an interview with Spanish television.
"Our idea was to avoid conceding a goal, which is important in a first leg at home, but our fourth will probably turn out to be very important," added the former Real Madrid striker, who is hoping for a callup to the Spain squad for this year's European Championship finals.
Barca came from a goal down to beat Real 2-1 on Wednesday, Carles Puyol and Eric Abidal netting after Cristiano Ronaldo had put Jose Mourinho's side, who beat their arch rivals 1-0 in last year's final, 1-0 up in the 11th minute at the Bernabeu.
On the other side of the draw, Athletic Bilbao have a 2-0 advantage over Real Mallorca after the Basques won Wednesday's first leg at the San Mames.
