Webber had come in to the Chinese Grand Prix eager to get a good result on the back of the troubles in Malaysia, when Sebastian Vettel ignored team orders and beat him.
But Webber's weekend was beset by drama, as a lack of fuel in his car during qualifying left him at the back of the grid for the race, and his Sunday afternoon ended after a pit stop problem resulted in a wheel falling off.
Speaking to reporters after the race, Horner was angered that there was even a suggestion that Red Bull was moving to try and hamper Webber's efforts.
"That is complete rubbish," he said. "Forget conspiracy. It is all about trying to get two cars to finish as high as we can.
"Anybody that thinks there is a conspiracy here against one, or either, driver doesn't know what they are looking at."
When it was put to him that Webber himself had not gone as far as ruling out a conspiracy, Horner said: "Mark knows exactly what happened. That is it. There is no conspiracy."
Red Bull was still awaiting a full analysis of Webber's car on Sunday night in China to work out why the wheel had fallen off, while the faulty fuel bowser that prevented enough fuel going in the car for qualifying will be looked at back at the team's factory.
"It will be stripped back down at Milton Keynes and investigated there," explained Horner.
F1 group editor Jonathan Noble
Although the cynics may suggest that Red Bull would obviously deny a conspiracy - even if there was one – fans should really forget any thoughts that Webber's Chinese GP nightmares were a deliberate ploy to hobble the Australian.
It makes no sense at all for an outfit to invest nearly £200 million per year on its two car operation and then throw half of its efforts away by deliberately stopping one of its drivers.
To suggest that the team would purposely not put enough fuel in Webber's car for him to complete qualifying is ridiculous, as there is no benefit to the team's constructors' championship ambitions by having one of its men at the back of the grid.
In fact, the conspiracy theories would actually have more credibility if the team had done the opposite and put too much fuel in Webber's car – thereby deliberately adding extra weight to the car which would have slowed him down and left him behind team-mate Sebastian Vettel.
Webber can look back at how straight the team played his battle with Vettel in Malaysia a few weeks ago – when a super swift final pit stop ensured he kept a slim lead over his team-mate before the 'Multi 21' controversy – for proof that the team does all it can to treat both men equally.
It is clear that Red Bull advisor Helmut Marko is politically fully in the Vettel camp, but when it comes to on track stuff, do not imagine for one second that the stance extends as far as derailing a driver by not giving him enough fuel or only three wheels.
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