The latest controversial flashpoint between the championship contenders occurred as Hamilton and Verstappen battled for the lead in Brazil shortly after the final round of pit stops.
Hamilton launched an attack around the outside of Verstappen at Turn 4, and was marginally ahead going into Descida do Lago, before the Red Bull driver ran both of them off the track.
The incident was noted by the stewards but was not investigated further.
Hamilton eventually found a way past Verstappen to complete a sensational comeback victory after starting 10th on the grid.
Mercedes boss Toto Wolff said it was “laughable” that Verstappen was not handed at least a five-second time penalty, but Horner disagreed.
“It is two guys running hard,” Horner told Sky Sports. “Lewis has got a run around the outside, Max has gone in deep and they have both gone wide.
“So it would have been really unfair to penalise on that.
“If it was the other way around, I would have let my sporting director have a moan about it but I wouldn’t have expected anything from it.”
Horner was adamant there was no lasting advantage to be gained by Verstappen running both drivers out wide, despite the fact the Dutchman was able to retain the lead.
“A penalty for what?” Horner said. “There is no advantage gained and no contact that has been made.
“It is just hard racing between the two of them. I think actually the stewards made the right decision on that.
"We have talked about this many, many times about the let them race mentality, and I think they made the right call today.”
And Horner reckons hard racing should be expected from two drivers battling it out for the world championship in the closing stages of the season.
“You know with Max, he is going to race hard and Lewis is exactly the same,” he added.
“That is two guys fighting for a world championship so it is going to be tough racing. But I think it was fair and there was no contact and they recommenced it a few laps later.”