The Kawasaki rider, who won race one on Saturday, added a second victory of the weekend at the Autódromo Internacional do Algarve.
It was a seventh consecutive race win at the circuit for Rea and his sixth straight victory this season.
Northern Irishman Rea won a battle with the Ducati of Chaz Davies to win with the Yamaha of Michael van der Mark finishing second and Ducati’s Marco Melandri finishing third. Welsh rider, Davies, who had battled through the pain barrier to race in Portugal following surgery on a broken collarbone suffered in a training accident, finished in fourth.
Rea’s win in the first race had seen the other two places reversed with Italian Melandri finishing second and Dutchman Van der Mark finishing third.
Rea heads the standings by 116 points from Davies with Van der Mark in third.