Defending World Cup winner Marciello led the 12-lap race throughout in his Team Landgraf Mercedes-AMG GT3, staving off a stern challenge from brand stablemate Maro Engel.
Edoardo Mortara completed the podium in his Audi R8 LMS GT3, having been passed by Engel on the run down to Lisboa at the start of the race.
Poleman Marciello managed to maintain his advantage on the opening lap, but the safety car was soon deployed when Porsche pair Thomas Preining and Matteo Cairoli both came to a halt at San Francisco.
The race resumed on lap five with Marciello leading Engel, Mortara and Daniel Juncadella, who tried to challenge Mortara heading down to Lisboa in a bid to make it a Mercedes 1-2-3.
But the move backfired and Juncadella was squeezed into the wall, and although he managed to continue he slipped to ninth place.
Out front, Marciello had stretched out a slender advantage of seven tenths of a second when Audi driver Adderly Fong suffered a huge crash at Mandarin on lap eight, bringing out the safety car a second time.
The race was then suspended while marshals repaired the barrier, with action only resuming 23 minutes later for a two-lap shootout.
Marciello managed to fend off Engel for the crucial run to Lisboa at the restart, and pulled away to the tune of 1.172s to claim victory and give himself pole for Sunday's main event.
Mortara held on to third ahead of Augusto Farfus in the best of the BMW M4 GT3s.
Sheldon van der Linde made it two BMW drivers in the top five when he passed the Ferrari 296 GT3 of Daniel Serra approaching Lisboa at the final restart, which was the only change of position in the top 10 after the red flag.
Behind Serra, Laurens Vanthoor was a low-key seventh for Porsche, having slipped from fourth on the grid after being nudged out wide at Lisboa on the initial start.
Christopher Haase (Audi), Juncadella and Earl Bamber (Porsche) rounded out the top 10.
Results to follow
