The two drivers both had the option to run either a medium/hard or hard/medium one-stopper combination.
From pole, Perez was in effect obliged to start on the medium as he couldn't risk losing out off the line to those around him, while starting ninth after a mistake in qualifying Verstappen had more freedom and opted for the hard.
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Red Bull's simulation numbers suggested that Perez's strategy would be around three seconds faster over the race distance.
However, Verstappen was able to produce unexpectedly good lap times over his long first stint on the hard tyre, even outpacing Perez on his much fresher set of hards after the latter had pitted.
Having emerged from his own stop just behind Perez on his new mediums, Verstappen wasted little time in hustling his way into the lead.
Horner suggested that Verstappen would have been equally impressive had he run the same strategy as his team-mate, given the form that the world champion displayed.
"I think if he'd been on the other strategy as well the performance would have been very similar today," he said.
"I think he was obviously frustrated with himself after quali, that he made a mistake, and then obviously didn't get the chance to rectify that.
"And I think he was confident coming into the race today, and just wanted to do something slightly different."
Horner confirmed that he was willing to support Verstappen's choice of strategy, even if it was theoretically slower.
"The strategy obviously is discussed, all the numbers are run overnight, and we weighed up the pros and cons," he said.
Source: Autosport