Netherlands, who visit Estonia on Friday, top the standings with 18 points from six games, followed by Romania on 13 from seven matches. Hungary are third with 11 points from seven games.
The home side took control with their first attack when Ciprian Marica stole the ball off Richard Guzmics, came face to face with keeper Adam Bogdan and calmly slotted home in the second minute for his third goal in the qualifying campaign.
Romania continued to press forward and Mihai Doru Pintilii doubled their lead with a thunderous 25-metre shot that gave Bogdan no chance after 31 minutes. It was Pintilii's first international goal in 14 appearances.
Bogdan Stancu almost got his name on the scoresheet midway through the second half but embarrassingly missed the target from the edge of the penalty area with only keeper Bogdan to beat.
Hungary came closest when Razvan Rat made a vital interception to deny Daniel Bode and Cristian Tanase made it 3-0 with a class finish with two minutes remaining.
Romania host Turkey on Tuesday in their next qualifier and Hungary take on Estonia.