Leclerc led for the opening stint of the race, but lost his lead when he was undercut by teammate Sebastian Vettel. However, after catching back up to him rapidly, Ferrari asked Vettel to let Leclerc through.
"At the start of the season, when we at least tried, it was not very well accepted from the outside," Binotto said. "But since the start, we've always said that the first priority is the team and the team's points.
"Race by race we normally are discussing with the drivers what may be the situation. It is something that we discussed in the morning.
"No doubt after a few races, things become more straightforward. Even when discussing with drivers, the drivers are more understanding.
"So it was never an easy call, because the drivers are in the car, trying to drive as fast as they can, trying to get as much points for themselves.
"But I think there were not many choices today. We had to anticipate a call and pit [Vette] to protect against Mercedes, otherwise, Hamilton would have stopped and it would have overcut.
"Also staying out put Charles in a better position with his tyres. He would have overtaken anyway because of the different strategy.
"They were on different strategies and earlier we swapped, we were losing time. It was the best [decision] for the team, and for Charles on that occasion."
The win also marks Binotto's first as Ferrari's team principal - however he brushed off the achievement, stating more praise is desvered for Leclerc and the team as a whole.
"To be honest, I don't think my first victory as team principal really counts," he said. "I'm more happy for Charles, more happy for the team.
"I think if there is any applause, it's to them. We are working as a team, and roles don't matter. Today we proved that the strength of the team can be very important."
Bahrain International Circuit - Winter testing