Halfway through the 2012 Formula 1 campaign Webber was Red Bull's main title threat, holding second in the standings, 10 points clear of Vettel.
But in the second part of the year Vettel surged to a third championship while Webber tumbled to sixth.
After Red Bull introduced a major upgrade for Singapore, Vettel claimed four straight wins and 141 points, whereas Webber's tally from the remaining rounds was just 47 points.
Horner acknowledged that the change in car spec could have played to Vettel's favour.
"Certainly Seb was able to get more out of the upgrade than Mark was," said the team chief.
"It did seem to suit his requirements whereas Mark never seemed quite as comfortable. But he still had Korea pole, a front row in Abu Dhabi, and outqualified Seb in Brazil.
"It was mainly in the races where Seb was able to exploit the most out of the car."
He felt the opposite had applied at the start of the season, when Webber was often Red Bull's lead runner.
"Certainly at the beginning of the year with the pre-Melbourne upgrade Sebastian was not at all comfortable, but he was still scoring strongly so when we did get the performance in the car he was able to capitalise on that," Horner said.
Although Vettel has become established as Red Bull's number one with his run of championships, Horner believes the battle between his drivers is as close as it was between erstwhile McLaren duo Jenson Button and Lewis Hamilton.
"I think it varies from track to track, condition to condition," said Horner. "In Brazil, between Lewis and Jenson it was swings and roundabouts between different points of the race.
"Some of that is style, some of that is lines used, but the same thing applies as the car develops - one driver will sometimes get more out of it than the other."
He added: "It's obviously tough for Mark - he is a world class driver but he is up against the best in the world. It is hard for any driver to accept that."