Leclerc qualified on pole seven tenths of a second ahead of Vettel, while the German struggled to hang onto his team-mate's coattails in the race, battling Lewis Hamilton to keep hold of second place.
After his tyres dropped off, Vettel was forced into a two-stopper, which dropped him to fourth place behind Hamilton and Mercedes colleague Valtteri Bottas.
Vettel said he was simply unable to keep life in his tyres around Spa-Francorchamps, but did not know why.
He said: "I didn't have the pace. I didn't feel comfortable with the car. I was going through the tyres way too quick.
"I was struggling to feel the grip, to stay on top of the tyres, I was sliding too much. It was quite a tough race for me.
"And obviously from that point where we came in quite early it was clear that we won't be there until the end. I guess I was sliding more [than Leclerc] but I don't know why."
Ferrari team principal Mattia Binotto suggested that the Scuderia may have been as much to blame for Vettel's struggles as much as the driver.
He said: "Sebastian suffered more with degradation this weekend, on Friday and during the race.
"It's certainly down to the set-up as well. Seb is normally very good at managing the tyres. Especially in the very first laps, somehow to use the tyres later in the stint.
"So it's something we will take care to try to understand and analyse. And if we may learn it we will try to improve ourselves for the future.