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.
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.
"His engineering team and Max were keen to give that a run today. I was happy to sign it off and say if that's what you want to do, then okay."
Horner suggested that Perez would be satisfied to have logged a second place, despite losing out to someone who started ninth.
"I think it's swings and roundabouts of sport, isn't it?" he said. "A week ago he was on a high. But I don't think he'll be too disappointed.
"He's still taking away 18 points from here. I don't think there's anybody that would have beaten Max today."
Horner explained that Perez didn't build enough of a buffer in his opening stint on the medium tyres in part because he was initially protecting his front right tyre.
He acknowledged that in retrospect the Mexican could have pushed harder on that set.
"The first 10 laps, he was very much managing the pace," said Horner. "And I think he was nervous about the front right. And as we started to see other teams start to get a bit of graining I think he was driving well within himself and the car to protect that front right.
"And then he started to push after the first 10 laps and start to build a lead.
"And I think probably with 20/20 hindsight, I think if you looked at the race again, he could have pushed harder in that in that first stint, because the medium tyre actually turned out to be a very good tyre as we saw with Fernando [Alonso] actually going quite a long way."
