The game was called off in the eighth minute on Sunday with fog cloaking Nacional's hillside stadium in Madeira, the fourth league game to be postponed on the island this season and the second involving the Portuguese title holders.
Benfica's win pulled them level on 40 points with second-placed Porto in the Primeira Liga, four behind leaders Sporting.
The match re-started at midday on Monday with only a few hundred people in the stands despite free admission, Portuguese media reported.
Jonas put Benfica ahead in the 23rd minute, the 15th after the re-start, with a looping header at the far post from Mehdi Carcela-Gonzalez's cross.
Soares equalised five minutes into the second half with a weak shot which wrong-footed Julio Cesar and trickled over the line before the Brazil World Cup goalkeeper could clear it.
Jonas, who made the last of his eight appearances for Brazil in 2012, put Benfica back in front from Raul Jimenez's cross in the 57th minute before heading in Andre Almeida's pass.
Greek forward Kostas Mitroglou completed the scoring in the 89th minute as the mist again began to descend over the Choupana stadium.
(Writing by Brian Homewood. editing by Ed Osmond)
