VW's third driver kept the 2014 Polo for the opening rounds while team-mates Sebastien Ogier and Jari-Matti Latvala had the first available examples of the latest car.
Mikkelsen got the upgraded machine for Portugal, and having topped Thursday morning's shakedown, he outpaced Ogier by half a second to win the Lousada superspecial too.
It was an all-VW top three, with Latvala three tenths slower than Ogier.
Jari-Matti Latvala beats Sebastien Ogier to claim win in Portugal
On his return to the WRC after missing Argentina, Robert Kubica took the new M-Sport Ford to fourth place.
That was a much better result than M-Sport's 'factory' drivers achieved, as Elfyn Evans and Ott Tanak were only 11th and 12th fastest.
Thierry Neuville completed the top five for Hyundai, ahead of Argentina winner Kris Meeke.
Ogier closes on Latvala in Portugal
Jari-Matti Latvala builds Rally Portugal lead