Toto Wolff believes the second place went begging for Valtteri Bottas, after a software glitch slowed the Finn's Mercedes in the closing stages.
Bottas had fallen down to third place behind Red Bull's Verstappen after a small error on his outlap on the hard tyres, with the Finn latching onto the back of Verstappen after his tyres got back up to temperature.
However, any chance of stealing the position back went away when Bottas slowed with an apparent issue that was quickly resolved on the Mercedes pitwall.
“I think, based on our speed on the straights, he might even have managed to pass [Verstappen]," Wolff told Sky Sport Italia.
"The problem was we had a little gremlin in some engine software that we wanted to eradicate, and that did just the opposite. That is something that we have to fix in our software."
Mercedes' straight-line speed appeared to be the deciding factor between Red Bull and Mercedes, with Hamilton able to swoop past Verstappen after a small mistake from the Dutch driver shortly after the Safety Car withdrew.
“We have a good top speed on the straights today," Wolff said.
"The set-up we chose was the right one. A little to the detriment of downforce and drag, but quick on the straight. That worked well, ”
With Mercedes arguably slower than Red Bull at the first two races, that seems to now be firmly in the past with the W12 so quick at Portimoa.
Wolff still believes it's neck and neck, though, saying, “The car was strong yesterday, which is a positive development. It's hard to say today, but I think both teams are on an equal footing. And you have to take P1 and P3 with the fastest lap."