Max Verstappen closed in on teammate Perez and passed him for the lead on Lap 15 after Perez was instructed not to fight the reigning world champion for position.
Verstappen eased to a comfortable victory following Charles Leclerc’s retirement to lead a Red Bull 1-2 in Baku and move into a commanding position in the world championship, 21 points clear of Perez.
It marked the second time in three races that Perez has been told to let Verstappen by, after they swapped places at the Spanish Grand Prix.
Asked by Crash.net if Red Bull would continue to use team orders or allow their drivers to fight, Horner replied: “I think today wasn’t strictly team orders.
“It was just a question of you’ve got a faster car and a slower car and Max had a significant pace advantage on Checo at that point and Checo had quite heavy graining on his tyres.
“So it was a question of ‘guys, let’s not put each other against the pit wall here if one car is quicker, concede and let’s focus on getting the best result for the team.’”
Horner admitted that the memory of Verstappen and then teammate Daniel Ricciardo’s crash at the 2018 Azerbaijan Grand Prix had been playing on the team’s mind.
“The pace difference between the two drivers was so significant,” Horner added. “We’d discussed it this morning that if you are racing, just give each other space and they did that today.
“2018 isn’t too far away at the back of our minds. So it was very important that the drivers, at this stage of the championship, are fair with each other because the priority is to maximise the points against Ferrari.
“We know they’ve got a very quick car at the moment and we’ve seen how quickly things can turn around, so as a team we need to prioritise that.”
After the race, Perez accepted that Red Bull’s call was the right one given he was struggling to match Verstappen’s pace during the opening stint.
"Max was a lot stronger today,” the Mexican conceded. “It was a good team result. It was the right call by the team because, at that time, Max was further ahead.
“In this place, anything can happen but we managed a 1-2 which is a great team result.”
Horner praised Perez’s maturity for understanding and put his early pace struggles down to rear degradation that Red Bull suspects was exacerbated by his qualifying set-up.
“I think Checo, he’s a mature guy and he gets the bigger picture and that it’s a long championship,” Horner said.
“He’s in the form of his career off the back of Monaco and his qualifying performance yesterday.
“I think maybe, with the benefit of hindsight coming into this weekend, perhaps there was too much weight put behind his qualifying set-up with the rear deg that he experienced.
“So that’s something to look at because Max was certainly in better shape in the race than Checo was at the back end of that first stint.”