Vettel is set to start the first race of the season from 11th position while Leclerc could only improve to seventh in the final stanza of qualifying at almost a second slower than pole-sitting Mercedes driver, Valtteri Bottas.
Ferrari underwhelmed during pre-season testing and, having opted to wait until it can introduce wholesale changes at Round 3 in Hungary, had played down its chances of a strong performance in the season-opener.
Even then, Vettel did not expect it to be found so wanting at the Red Bull Ring.
“Obviously it's a surprise,” said the German.
“We thought we had a little bit more in hand, but it looks like the others were probably running a bit more fuel, a bit more conservative in practice.
“I wasn't quite happy with the car, I was not so happy with the car, quite more oversteer on entry than I would have liked. But we'll see.”
He does, however, expect a better outing in Sunday's 71-lap race.
“Tomorrow is a different picture,” stated Vettel, who will start one spot behind Daniel Ricciardo.
“I think with the track getting a bit hotter, it was a bit more costly for us today.
“It's a long race. I think in race trim we are always better. I think we will be there to make up some good ground and score some good points.”
Ferrari almost suffered a double exit at the end of Q2, when Leclerc, last year's pole-sitter in Austria, was 10th.
The Monegasque wound up 0.984s away from pole, while Mercedes enjoys a front row lockout with Lewis Hamilton only 0.012s slower than Bottas.
Race start is scheduled for 23:10 AEST.