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."
Verstappen said he was confident that his decision to start on the hards, compared to mediums for the cars on the front three rows, would pay off the way it did.
"We started talking about it yesterday," Verstappen said about his winning tyre strategy.
"We didn't know what the weather would do, but we were quite confident that this will pay off and luckily it did today.
"I picked the cars off one by one and then I could stay out really long on the hard tyres. And that's where we made the difference today, and then a good little battle with Checo at the end.
"Yesterday was of course a bit of a setback, but today we just kept it calm, kept it clean. Winning a race from P9 is always very satisfying."
Verstappen's emphatic win is a hammer blow for Perez after the latter gained momentum by winning last week's Azerbaijan Grand Prix.
In Miami the reigning world champion extended his lead from six to 14 points, having also secured the bonus point for the fastest lap.
