Ferrari caught Red Bull by surprise after Sergio Perez recorded a shock win in a rain and crash-marred Monaco GP.
Boss Christian Horner was talking to the media about his Mexican driver's win when he took an urgent phone call from team manager Jonathan Wheatley.
"Ferrari just lodged a protest against Max," the Red Bull chief told the reporters.
His Ferrari counterpart Mattia Binotto explained: "We lodged the protest because we wanted clarification.
"It's not directed at Red Bull itself - we believe that both Red Bull cars have touched the (pit exit) line. This has always been a penalty in the past."
The FIA ultimately sided with Red Bull, compounding the disappointment about Charles Leclerc's championship gap to Max Verstappen blowing out further to 9 points.
Monaco local Leclerc was furious, prompting suggestions that the Maranello team had "let down" its lead driver with poor strategic decisions.
"Let down is not the word - some mistakes can happen. But there have been too many mistakes," former championship leader Leclerc, 24, said.
"We cannot afford to do that, especially in the moment we are in, when we are extremely strong."
A contrite boss Binotto admitted: "It is obvious that our decisions were not the right ones."
Top Red Bull official Dr Helmut Marko shrugged his shoulders when asked how the energy drink owned team kept its strategic cool while Ferrari blundered.
"I don't know what information they had," he said. "We did what we had to do.
"Our strategic people had everything under control and handled the situation wonderfully. That we managed to split the Ferraris and finish ahead of Leclerc - we are more than happy with that."
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