An inspired call to switch to intermediate tyres before anyone else during an early downpour saw Perez rise from seventh on the grid to move into the race lead.
Polesitter Verstappen switched onto inters slightly later and subsequently dropped to fourth, though he made short work of cutting through the field and reeling in his teammate.
Verstappen was back in the lead on Lap 13 after Red Bull called him in to pit for slick tyres a lap before Perez, resulting in the Dutchman successfully pulling off an undercut.
The reigning world champion went on to claim a record-equalling ninth successive victory and score his 11th win in 13 races this season.
“The way he [Verstappen] cut through the traffic was quite sensational,” Horner said.
“Checo had the target to pull the gap on the cars behind him but Max’s pace as he came through the field was such that at one point he took seven seconds out of him over three laps. And was coming very fast.
“Then you get to that awkward point at the crossover and [Fernando] Alonso and [Pierre] Gasly behind him had pulled the trigger after [to switch to slicks].
“You could see from Albon [on slicks] that the circuit was coming alive for the slicks.
“So had we pitted Checo first they would have both undercut Max so we’d have gone from a net one-two to a net one-four. So we pitted Max first with the risk that he’d undercut Checo but we’d end up as a team first and a second.
“It was a no-brainer.”
Perez, who slipped to fourth after a spin and time penalty for speeding in the pit lane, sounded confused over the team radio when he re-emerged from the pits in second place, asking: “did Max undercut us?”
But the Mexican downplayed the decision after the race.
“Well, I think in those scenarios the team just have more information than we do at the time,” Perez said.
“It’s something we obviously will review during the meeting. I’m sure there’s a reason behind it.”