When announced that Vettel would leave Ferrari at the end of the 2020 season, rumours suggested the German had been unhappy with the contract offer put forward by Ferrari.
Both the pay packet and the contract length were called into question.
"No, that is not true," Binotto told Marca. "It is simply that things have changed, and we are looking at a new cycle, and it seems that this vision, in terms of timing, did not coincide with its vision. It was not because of the type of offer or its duration."
He added: "Without a doubt, for many reasons, Ferrari loves Sebastian as a driver and as a person, he is part of our team, our project, so it is never an easy decision.
"Seb was our first option and then the Covid arrived, a situation that has changed many things, from the regulation to the budget ceiling, things that have changed the vision of the situation, looking ahead as with the new car, postponed to 2022.
"Difficult internal reviews had to be done, and that's what we did."
Vettel has since been linked with drives at Racing Point, the team to become Aston Martin in 2021, Renault, and Mercedes.
Binotto said: "I hear rumours that you can find him in Mercedes and I would be very happy for him, I really would be."
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