Tensions between the two drivers have grown since Vettel ignored team orders to pass his teammate in the Malaysian Grand Prix last month.
Suggestions of a conspiracy have further gathered pace after Webber had a problem-hit time at the Chinese Grand Prix, leading to a wheel falling off during the race.
"That is complete rubbish. Mark knows exactly what happened. Exactly. That's it. There is no conspiracy. Forget conspiracy. It is all about trying to get two cars to finish as high as we can," Horner told reporters at a press conference.
It is widely thought that Webber will leave Red Bull at the end of the season.