Sebastian Vettel came home third ahead of team-mate Charles Leclerc, but both conceded that they could not generate the pace to compete with Hamilton's Mercedes or the Red Bull of second-placed Max Verstappen at the Hungaroring.
"It's very track dependent," said Binotto. "Our car is lacking in maximum down-force so when you are at a circuit, like Budapest, where maximum down-force is needed, then we suffer.
"And we're suffering more in the race than in the qualifying because, in the single lap of the ‘quali’, eventually the grip of the tyres is coping with the lack of down-force you have.
"But on a long distance run, you're sliding, overheating the tyres and things are more complicated."
Ferrari chose to give priority to aerodynamic efficiency in the creation of their 2019 car – a move that should favour them at fast, low down-force tracks like Spa-Francorchamps and Monza, where the upcoming Belgian and Italian Grands Prix take place next month.
Both four-time champion Vettel and Leclerc brushed aside suggestions after Sunday's race that the intensity of the duel for victory had lifted the pace of the contest.
"I think they were pushing flat out and we were pushing flat out," said Vettel. "So I don't think they were able to get another second just because they enjoyed themselves."
Leclerc said: "No, I don't think so either – we were pushing at the maximum to try to have our best race."