Leclerc and Max Verstappen had been battling each other early on after the restart in wet conditions, until the Red Bull driver got well ahead after the Ferrari's intermediate tyres wore down. Leclerc was then left to fend off the attacks from third-placed Sergio Perez in the last 10 minutes of the race.
Heading into the last lap, the Red Bull driver was strongly challenging second-placed Leclerc but a mistake at the final chicane saw the Ferrari driver cut the corner and then squeezing Perez down the home straight to the finish line to claim second place.
The race stewards then stepped in to hand Leclerc a five-second penalty which in-turn saw the drivers swap positions and Perez claimed second place ahead of the Ferrari driver, meaning Verstappen became a double-world champion.
What has annoyed Ferrari boss Binotto is the lack of consistency shown by the FIA in decision-making, when it took around five-hours last week in Singapore for the outcome to be announced over an investigation of Perez' safety car protocol breaches.
"Very surprised, very disappointed," said Binotto after Sunday's the race.
"The reason why, I think that seven days after Singapore, while there it took so many laps to decide and then even after the race, we had to hear from the drivers to take a simple decision which was straightforward.
"Today, they took it in a few seconds. Surprised by such a difference between Singapore and here after only a few days."
When asked about how valid he thought the Leclerc penalty was, Binotto said: "In our view, he didn't gain any advantage.
"He was ahead, he stayed ahead and kept the same gap. It is still arguable but that is the way they decided which we will accept.
"Certainly, very frustrating to see such different timing in decisions and at least in such a situation, why are we not listening to the drivers like in Singapore or vice versa?
"If you go straight for a decision, as obvious as it should be, the five seconds in Singapore should have been given immediately which would have given us the opportunity to manage the situation differently and it could have been a potential victory," Binotto added.