He saw off competition from Toprak Razgatlioglu and Michael van der Mark who finished second and third respectively.
Rea was barely challenged as the drama unfurled behind him, with Scott Redding moving from eighth up to third before Michael van der Mark edged ahead in the final laps.
Redding remains ahead in the overall standings after his double win in Jerez, Spain with 107 points last weekend, but Rea is just eight behind on 99.
Rea had claimed Tissot Superpole as Redding suffered a costly crash
The Series Rookie Redding took a tumble at turn five.
It was Rea's fourth pole at Portimao, more than any other World SuperBike rider.