Verstappen started the race 16th on the grid after an engine penalty but scithed his way through the field.
And having gambled on a two-stop strategy, the Dutchman was finishing the race on fresher tryres and surged past Kimi Raikkonen on the final lap to claim third.
However, the stewards deemed him to have gained an advantage by having all four wheels off the race-track and gave him a five-second penalty, relegating him to fourth.
But Red Bull boss Horner, who had watched Verstappen’s team-mate Daniel Ricciardo retire with an engine failure, was even more frustrated by the stewards’ decision.
“There’s been cars going off track all day today and there’s been no action at all so I think it would be unbelievably harsh to give Max a penalty for that,” Horner said after the race.
“It just doesn’t feel right.
“It’s wrong. We’ll have a look at it but for that was fair, hard racing.
“That’s a bad judgment by the stewards.”
He added: ”It is an appalling decision.
“They have robbed all of the fans here.
“It was a great Grand Prix and they have screwed it up.”
Mercedes’ Niki Lauda waded into the debate by saying: ”They shouldn’t intervene in situations like that. It was a normal overtaking move. You can’t be more stupid than that.”