Rosberg got by the Red Bull driver between turns eight and nine in a move that could be said to have clinched the title for Rosberg.
"Nico was quite brave on the move that he made on Max," said Horner. "It looked like he decided to get on with it at that point, we know Max isn't the easiest car in the paddock to overtake. For me, that was the deciding moment in Nico's race."
Prior to the Brazilian Grand Prix, Verstappen was asked by Mercedes boss Toto Wolf not to interfere with the title fight involving both Silver Arrows following a number of on-track controversies.
Rosberg and Verstappen's battle on track could have made a few in the Mercedes camp nervous, with Horner believing Rosberg had been instructed to avoid the teen sensation.
"It looked like Rosberg was being instructed not to go anywhere near Max," said the Red Bull boss. "While he was doing that, obviously that was making the one stop become more and more available.
Bahrain International Circuit - Winter testing