The Italian outfit went into the race four points shy of Mercedes and needed both cars to score well in order to make up the deficit.
But while Charles Leclerc took second place behind Max Verstappen, his team-mate Sainz failed to log any points. With George Russell earning third and Lewis Hamilton taking ninth, the Brackley team stayed in front.
After a frustrating Q1 session saw Sainz qualify 16th, Ferrari put the Spaniard on hard tyres at the start. However, he lacked pace and the team stopped him earlier than planned and gave him a second set of the same compound.
He was thus committed to a second pit visit for mediums, and the team left him out until the last minute in the hope that a safety car would give him a cheap stop.
In the end that chance didn't come and Sainz came into the pits on the penultimate lap, having dropped out of the points he was officially retired with what the team indicated was an engine problem.
Vasseur said that the strategy wasn't to blame for his poor race and that Sainz, who had a big crash in FP2, was simply missing pace.
"When you have to pit on lap 20, you have no other option than to put on a second set of hards because if you put on mediums, you will have to pit on lap 30," he said.
"And the plan was – I don't know if it was a plan – but the option was to put hard-hard and to expect that we would have a safety car or red flag.
"The issue is that it was not a matter of strategy, it was a matter of pace. We did not have the pace today, and in this case, all the strategies are the bad ones."
Regarding the originally planned stop schedule for Sainz, he said: "Lap 35 or something like this, to the reverse of the others.
"The others did 15-20 laps with the medium and then 40 laps with the hard, and the target was to do 40 laps with the hard with part of the race in clean air and try to compensate part of the deficit."
Vasseur insisted that starting on the medium rather than hard would not have made a difference.
"You can always try to redo the race and to say that, but I don't think so," he said.
"I think the issue was the pace and was not the hard or the medium. He was on track with the same tyres as Charles. We had an issue, and need to understand the issue. It was not the strategy at all."
Expanding on the lack of performance he stressed that the championship outcome wasn't decided solely at the finale.
"For sure Carlos was out of the pace today, that is clear, and we have to understand why," he said.
"But honestly, it's not today that we missed something. If you have a look on the championship, I think we had tough events.
"We had Miami, we had Zandvoort in terms of pace, and we had some events when we had a reliability issue, and this was much more painful than today.
"Today we had a strong pace as a team, we are able to fight for the pole position yesterday. We fought with the Red Bull almost all the race. I'm not sure that it's today that we missed something."
