The 24-year-old, who is attempting to win his first F1 title, was handed a 10-second penalty for the incident, where Hamilton drove into the back of his car.
Verstappen had been ordered to give the place back following an earlier moment of controversy when the Dutchman forced the seven-time champion wide.
“He’s certainly not crazy,” Horner told The Times. “You’ve got two guys, different ages, going for the biggest prize in motorsport.
“Lewis is 36 and going for his eighth world title. Max is attempting to win his first. And I think Lewis has an enormous amount of experience. He is using all of that. He’s a wily competitor.
“It’s frustrating. There’s been some confusion. Some incidents get punished, some go unpunished. Max does tend to get the harsher verdict, particularly when you look back at the weekend.”
The Red Bull boss added: “I think there was gamesmanship going on where Max had clearly lifted off and had gone down through the gears, to [a speed] slower than the slowest corner of the circuit, yet Lewis didn’t want to overtake, because he didn’t want to be the first to cross the DRS line.
“So he was desperately trying to avoid overtaking Max, who had been instructed to let him pass by the stewards, or by the race director and therefore by the team.”
Hamilton’s third victory in a row saw him move level on points with Verstappen ahead of the season-ending Abu Dhabi Grand Prix on Sunday.
However, as Verstappen has nine victories so far this season to Hamilton’s eight, the 24-year-old will win the championship if neither driver finishes the race.
But Horner was adamant that Verstappen will want to win the F1 title the right way and insisted he will not try and take out his title rival at the Yas Marina Circuit.
“Max wants to win this championship on the track,” Horner said. “It’s as simple as that. He’s a hard racer but a fair racer, and I expect no different this weekend. Nobody wants to win this championship in a gravel trap or in a stewards’ inquiry.
“To finish first, first you’ve got to finish. That’s been our mantra throughout this season.”
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