Christian Horner has told Mark Webber there was 'no conspiracy' nor 'malice' from Red Bull regarding the outcome of last Sunday's Malaysian GP.
Leading the grand prix, Webber was told to turn his engine down while team-mate Sebastian Vettel, who was running second, was ordered to hold station.
The German, though, ignored the order and snatched the victory from his Australian team-mate.
The matter thrust Red Bull into the headlines with reports claiming Webber is considering whether he wants to remain with team.
His boss, however, believes there is no reason to quit as Red Bull did nothing wrong.
"Mark knows the team didn't manipulate anything, there was no conspiracy," Horner told Sky Sports News. "It was the intent of the team that Mark win that race.
"We didn't suddenly give Sebastian instruction and say 'go and pass your team-mate'.
"He (Webber) is big enough to know there was no malice or intent from the team to create any situation like that.
"He is in a car capable of winning grands prix, and hopefully going for a championship, so I've no doubt Mark will see out the season with us."
Meanwhile, Red Bull advisor Helmut Marko believes the matter is closed and all is well between the two drivers.
"They don't have to be completely on the same page but it must be a solid working partnership," he told the Mirror. "Sebastian apologised in the press conference, and that's the first correct step to take.
"In the debrief afterwards there was the relevant discussions about the race and then there was a handshake between the two drivers. So, for us, now, the issue is settled."