The Portugal captain scored after he was set up by an outrageous backheel from Andre Silva and smashed in a long-range free kick in the second half. Silva had opened the scoring from a move in which Ronaldo also played a part.
The win kept the European champions three points behind Group B leaders Switzerland, who earlier beat Latvia 1-0 to maintain their 100 percent record with 15 points from five games.
Defeat left Hungary a distant third with seven points and only the slimmest of chances of their first World Cup appearance since 1986.
Portugal were nearly knocked out of Euro 2016 at the group stage by Hungary, having to come back three times to force a 3-3 draw.
But they had no such trouble this time despite a slow start in which Ronaldo shot over from a free kick and headed wide after Ricardo Quaresma's cross found him unmarked at the far post.
Just as coach Fernando Santos's decision to leave out Bernardo Silva appeared to be backfiring, Portugal went ahead.
Ronaldo released Raphael Guerreiro on the left and his low, first-time cross was turned in at the far post by an unmarked Silva in the 32nd minute.
Four minutes later, Pepe's long ball out of defence was met by Silva with a first-time backheel to Ronaldo who squeezed a low, left-foot between Peter Gulasci and the near post with stunning precision.
Brimming with confidence, Portugal's record scorer then tried to meet Joao Mario's dinked passed with a bicycle kick but did not get enough power behind the shot which Gulasci saved comfortably.
But he was not to be denied another goal and, inevitably, when Ricardo Quaresma won a free kick outside the area in the 65th minute, it was Ronaldo who took it.
Repeatedly criticised during Euro 2016 for his record from free kicks, he made no mistake this time as he scored with a vicious effort which dipped over the wall and bounced in front of Gulasci.
It was his 70th goal for Portugal in 138 appearances.
The group looks increasingly likely to boil down to Portugal's match at home to Switzerland in October.
Only the winners of the nine European groups go straight to Russia next year while the eight best runners-up go into a playoff round for four more places.
