Cristiano Ronaldo was also on target as Roberto Martinez’s side secured their second win from their two opening games against the spirited hosts, for whom Barnabas Varga netted twice in Budapest.
Portugal lead Group F on six points from Armenia on three after their win over the Republic of Ireland earlier.
“We knew it would be complicated, we made mistakes and allowed transitions,” said Bernardo Silva, who levelled for Portugal after Varga opened the scoring.
“It’s always difficult to find balance, probably one of the hardest things in football, especially against teams that defend with such a low block,” he added.
“Above all, it is a young team that is still growing, but the most important thing is the six points, and we took a giant step towards securing qualification for the World Cup.”
Nations League champions Portugal were high on confidence after thumping Armenia 5-0 on Saturday and dominated possession.
However, it was Hungary who took the lead as Ferencvaros striker Varga found a gap in Portugal’s defence and nodded home Zsolt Nagy’s cross.
Portugal responded by pouring forward and Hungary goalkeeper Balazs Toth made a stunning save to deny Ronaldo from close range after half an hour.
The visitors levelled six minutes later with Manchester City midfielder Silva lashing into the roof of the net after the ball broke his way in the box.
Portugal took the lead after 58 minutes through veteran striker Ronaldo, aiming to become the first player to feature at six different World Cup finals.
The five-time Ballon d’Or winner won the spot-kick when his shot was handled by Loic Nego, and he squeezed it into the bottom left corner beyond Toth’s outstretched fingertips.
Ronaldo became the player who has scored the joint-most goals in World Cup qualifying history, level with retired Guatemala international Carlos Ruiz, as he bagged his 39th.
Hungary, who last qualified for the World Cup in 1986 and have never beaten Portugal in 15 attempts, equalised with another Varga header from Nego’s cross after 84 minutes.
Just two minutes later Portugal stole the ball back high up the pitch and Cancelo stroked home to claim the three points.
“It’s hard to win when you concede two goals,” said Martinez. “I loved the attitude and focus. We just needed to control the game and take it where we wanted. It’s a perfect match for improvement.” (AFP)
