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.
Sordo picks final starting spot
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.
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Ogier charges clear in Portugal