Leclerc took his third pole in a row and led Sunday's race for 21 laps before a tactical decision from the team left the 21-year-old behind his German team-mate.
Ferrari called Vettel into the pits a lap earlier than Leclerc, handing the former a circuit on fresh tyres to wipe out the Monegasque driver's lead.
Seeing the Ferrari of team-mate Vettel ahead of him after emerging from the pit lane, a furious Leclerc said on team radio: "What the hell?"
After a word of assurance from a Ferrari engineer, he added: "To be completely honest, I don't understand the undercut at all. But we discuss it later."
Ferrari team boss Mattia Binotto later said there was "no discussion" to be had over whether it was the right call to bring Vettel in a lap earlier.
Binotto explained that Max Verstappen, who was fourth behind Vettel, was ready to pit at the same time so the decision was made to protect the German's position.
He also said Ferrari's tactics presented them with the best chance of catching Lewis Hamilton in second.
"That was the right time to stop Sebastian - no discussion," Binotto said. "Going out he drove very well on new tyres and, simply, that's racing and he has been ahead of Charles."
"We could not have stopped Charles at that stage because if you are leading the race you will not stop first. It was simply the proper window for Seb."