Moussa Marega's 51st-minute strike proved the difference between the two sides, with the Toffees now having lost both games in the pre-season competition.
On 24 minutes, Cenk Tosun deftly controlled Seamus Coleman's cross before firing a shot from the edge of the area which came off against the woodwork.
Porto finished the half strongly, with Felipe's header forcing Stekelenburg into action, and shortly after the restart, Marega opened the scoring by breaking free and slotting low past the Dutchman.
Although Everton sought to draw level, with Tosun heading Ramirez's centre over the bar midway through the second half, Porto held on to secure the win.
The match was the Toffees' final game in Portugal before they take on Blackburn Rovers, Rennes and Valencia ahead of their Premier League opener at Wolverhampton Wanderers.
PORTO: Casillas, Pedro, Felipe, Leite, Telles, Otavio, Oliveira, Torres, Brahimi, Marega, Aboubakar
EVERTON: Stekelenburg, Baines, Keane, Jagielka (Holgate 75'), Coleman, Schneiderlin, Davies (Besic 87'), Dowell (Niasse 87'), Mirallas (Vlasic 71'), Ramirez, Tosun