Perez started from pole with Verstappen down in ninth after the Dutchman failed to set a lap in Saturday's Q3 qualifying shootout.
But starting on the hard compound, Verstappen effortlessly carved through the field on Sunday and kept his tyres alive until lap 45 of 57.
Verstappen's enduring hard tyre pace allowed him to almost lead by a pitstop when he finally came in for mediums.
Returning to the track just behind Perez after his switch to fresh medium tyres, Verstappen made short work of his struggling team-mate to take his third win of the season.
Perez said his race was lost on his initial medium stint as the yellow-walled tyre performed worse than expected and soon suffered from graining.
"I think the medium initially was really poor. Worse than expected," Perez said.
"The first stint was really poor with the graining that we had on that initial pace. And that compromised quite a lot of our race because we didn't have too much of a difference on tyre."
Perez also conceded that Verstappen put in a masterclass to beat him from ninth on the grid.
"Honestly, I think also Max had a tremendous pace on the hard tyre and I think I've got to analyse what went wrong today because we simply didn't have the pace," he added.
"Max was particularly strong today, so a well-deserved win for him."
Source: Autosport