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.
Malaga are sixth on 17 points after being held to a 0-0 draw at Andalucian rivals Real Betis with the big-spending south-coast club continuing to struggle to live up to expectations.
Promoted Betis, who were top of the table six weeks ago, earned their first point in seven outings, ending a run of six defeats in a row which has seen them plummet to 11th.
HARD AND FAST
It was the first time in nearly half a century that Levante had hosted Valencia while placed higher in the standings.
The tackles flew in hard and fast and the referee flashed five yellow cards before the break as tempers were never far from boiling over.
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.
Levante lost their first game of the campaign by the same scoreline 2-0 at Osasuna last weekend.
"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."
