Valladolid wins second straight match
The 24-year-old, who scored eight goals last season to help the Pucela to promotion, was on target in the 38th and 48th minutes on a fiery night in the north of Spain.
Referee Ignacio Iglesias Villanueva brandished six yellow cards and one red - that to Levante defender David Navarro - as tempers became frayed.
But Perez kept his cool amid the chaos to earn the points for Miroslav Dukic's side, pushing them up to six points and a share of the lead following their victory at Atletico Madrid last weekend.
His first goal came after Navarro was sent off for handball and his second following Papakouli Diop foul on Omar, as the Granotes were unable to get going.
Juan Ignacio Martinez's men remain on a point as a result and never looked like getting anything on Monday night.
Their hosts started the brighter at Jose Zarilla, with Javi Guerra's header drawing an early save from Gustavo Munua.
Angel Rodriquez tried to get Levante started with two shots that went over, but his efforts came to nothing when Navarro - already on a yellow - stuck an arm out in the box.
Patrick Ebert then forced Munua to tip a powerful effort over the bar as Vala pressed for a second, before Diop handed it to them three minutes after the break when he hacked down Omar.
Ebert went close as he looked for a third, while Perez spurned his chance of a hat-trick when he dragged wide.
Guerra should also have done better as the home side turned on the style, with Levante grateful to Munua for keeping the score down as he blocked Juan Neira's late, close-range effort.