Leclerc passed Vettel at the start but appeared to be struggling slightly more with his tyres than his four-time world champion team-mate, who he was eventually told to let past and did so at the start of lap 11.
It was the third time in three races that Ferrari has issued an instruction to Leclerc, having confirmed Leclerc needed to stay behind Vettel at the end of the season-opening Australian GP and telling him not to attack for the lead in Bahrain, where Leclerc passed Vettel anyway.
"Certainly it's difficult as a team to give the order," said team principal Binotto.
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"Because we understand the drivers, they need to battle to stay ahead as much as they can.
"It was certainly not an easy decision. I have to thank Charles. The way he behaved, it again shows he's being a good team player.
"But I think again there will be a time where the situation is simply reversed.
"As a team we need to maximise the team points. In that respect I think we did the right choice."
Leclerc said immediately after the race he wanted to wait to hear from his team before he commented on the swap.
Speaking to media later in the evening, Leclerc said of the early team order: "Obviously being in the car it was a bit frustrating but on the other hand I am well aware that in the car you don't see much of the full picture of the race.
"So then I just accepted it, did it, and focused on my race."
The result has moved Vettel ahead of Leclerc in the drivers' championship by a single point, but Ferrari's leading man is still 31 behind Mercedes driver, and new points leader, Lewis Hamilton.
Leclerc said he was satisfied with Ferrari's reasoning for the team order.
"It was not an easy situation," he said.

Sebastian Vettel, Charles Leclerc (Ferrari) - GP of China 2019

Image credit: Getty Images

I was obviously struggling with the tyres. We both were. And at the time it just felt like Seb was quicker.
"But obviously being behind me for some laps he obviously damaged his tyres and when he went in front his tyres were probably also damaged."
Binotto said that Leclerc's long second stint was primarily to assess the validity of a one-stop strategy, rather than hold up one of the Mercedes as Leclerc had previously suggested.
The strategy meant Leclerc slipped behind Red Bull's Max Verstappen into fifth, with Vettel on the podium.
On the early team order, Binotto added: "I think what we tried at the time, we tried everything we could not to lose time on the Mercedes ahead and that was the only chance we got at the time.
"We tried, it didn't work. It was right to give the chance to Seb.
"As a team we did whatever we could."
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