Porto had clinched their 25th title last month and completed the season with 84 points after 27 wins and three draws. They face compatriots Braga in the Europa League final on Wednesday and are also in next weekend's Portuguese Cup final.
Portugal international Varela fired Porto ahead after being put through by Colombia midfielder Fredy Guarin in the 21st minute while Walter headed home the second after 32 minutes.
A Benfica side led by Eusebio in 1973 had been the only undefeated Portuguese champions, and while the Lisbon club finished a campaign without losing in 1978, they did not win the title that season.
"Today we achieved something that is very difficult, and which will remain in our memories forever. We are very proud of our work," Porto coach Andre Villas Boas told SportTV.
Last season's champions Benfica drew 3-3 at home to Uniao Leiria to finish second on 63 points and will play in the third qualifying round of the Champions League next season, with Porto going straight into the group stage.
Sporting beat Braga 1-0 away to overtake the northern side and claim third place, with both clubs entering the Europa League qualifying stage next season.
Fifth-placed Guimaraes also have a Europa League spot having reached the Portuguese Cup Final, with opponents Porto already in the Champions League, so sixth-placed Nacional get a place in the qualifying rounds of Europe's second-tier competition.
Portimonense and Naval were relegated to the second division.
Porto's Brazilian forward Hulk was the top scorer in the league with 23 goals.
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