Citroen's Spanish star built on his Fafe Rally Sprint victory last Saturday with scratch time at the three-mile stage close to the rally's Faro base.
Sordo was seven tenths of a second up on Ogier and 1.3s faster than his team-mate Mikko Hirvonen.
"I don't really like that road, but the feeling in the car is really, really good. I am happy with the time," said Sordo.
WRC
Sordo picks final starting spot
11/04/2013 AT 12:55
Ogier is still suffering from the flu that ruled him out of Fafe and admitted, under the circumstances, he was happy with second.
His fellow Volkswagen driver Jari-Matti Latvala was third with top M-Sport runner and last year's Portugal winner Mads Ostberg fourth.
Portugal Rally
Ailing Ogier fears for Portugal fitness
11/04/2013 AT 12:29
Portugal Rally
Ogier charges clear in Portugal
13/04/2013 AT 17:26