An own-goal from Javi Venta and free-kick from Tino Costa after the break saw Valencia climb above their neighbours into third place on 24 points.
Levante are in fourth place a point further back.
"It was the game we expected in terms of intensity, competitivenes and tension," Valencia coach Unai Emery told reporters. "We managed it well against a team who had won every game at home."
Sevilla are fifth on 18 points after a drab 0-0 draw at a rain-soaked Real Mallorca, with Marcelino's side still to record a win on the road this season.
Mallorca's new coach Joaquin Caparros remains without a win since replacing Michael Laudrup early last month.
Tino Costa's clever ball behind the defence set Jordi Alba scampering into the area after 32 minutes, but as Levante full-back Venta slid in to tackle him he diverted the ball past his own goalkeeper.
Costa doubled the lead when home keeper Gustavo Munua completely misjudged the Argentine's free-kick after 50 minutes.
"I have to congratulate Valencia because they played a good game but the goals were hard to take especially the second," Levante coach Juan Ignacio Martinez said.
"We'll pick ourselves up. We have to think about now and not what could have been."
