In a patched-up McLaren sporting a new front wing and with parts bandaged with gaffer tape following a collision with Williams' Pastor Maldonado at the end of the middle session, Lewis Hamilton appeared to have grabbed his first pole since Canada last year.
But within seconds such pleasure was denied the Briton as reigning champion Vettel made it 24 poles in his career, beating his 26-year-old rival by almost half a second.
As for Michael Schumacher, on the 20th anniversary weekend of his Formula One debut at Spa, his qualifying session lasted just 90 seconds.
The seven-times champion hit a wet patch in his Mercedes which sent him skewering into a wall where he then lost a wheel, his car then sliding all the way down the hill into the gravel trap at Rivage.
Calmly over the radio the 42-year-old said: "I don't know what happened there, something unexpected. I'm out."
On a drying track, after the first two sessions were run mainly in the wet, Red Bull's Mark Webber was third - the Australian not quite adding icing on the cake of his 35th birthday celebrations and after signing a new contract extension for next season.
Ferrari's Felipe Massa starts fourth ahead of Nico Rosberg in his Mercedes, with Toro Rosso's Jaime Alguersuari sixth and Bruno Senna on his qualifying debut for Renault a superb seventh.
Fernando Alonso in his Ferrari could only claim eighth, with Sergio Perez in his Sauber ninth and the Renault of Vitaly Petrov 10th.
With under seven minutes remaining in second practice, the session was red flagged following Adrian Sutil's accident as he crested the brow of the hill coming out of the Eau Rouge/Raidillon complex.
Even in the wet the German was still travelling at considerable speed, but in putting a wheel on the kerb as he turned onto the Kemmel straight, that was enough to send him into a wall.
With debris on the track, race director Charlie Whiting was left with no alternative but to bring a temporary halt to proceedings whilst the marshals made the circuit safe.
The 15-minute run then ended in bizarre and controversial fashion, initially as Hamilton and Pastor Maldonado were involved in their second incident of the season.
The first was in Monaco when Hamilton hit Maldonado late in the race through Ste Devote, sending the Venezuelan out when he was on course for his first points of the campaign.
On this occasion, with Hamilton on a flying lap and desperate to get into the top 10 as he had dropped out at that stage, he bumped wheels with the Williams as he squeezed up the inside coming out of the bus-stop chicane ahead of the start-finish line.
After setting the third fastest time, Maldonado then appeared to exact revenge on the run out of La Source, clipping the McLaren.
In attempting to correct his car, Hamilton subsequently hit the 26-year-old, forcing the Williams off track whilst he trundled back to the garage for repairs.
Over the team radio Hamilton claimed Maldonado's actions were "done deliberately".
In a dramatic few moments for McLaren, the Woking-based team made a woeful error in calling in Button too early believing he had done enough.
However, the victor last time out in Hungary will start 13th behind Toro Rosso's Sebastien Buemi and Sauber of Kamui Kobayashi.
Behind him will be Williams' Rubens Barrichello, Sutil, Maldonado - if he is not excluded by the stewards - and Heikki Kovalainen in his Lotus.
The conditions also accounted for Paul di Resta's failure to make it out of Q1 for the first time this season.
Throughout the session, on a predominantly wet track, the times tumbled as a dry line slowly began to appear.
But just 90 seconds from the end, and with Di Resta setting his quickest times in the first two sectors, the rain struck again, initially over the start-finish area.
Approaching the bus-stop chicane, the Scot slid on entry, and although managing to recover, he finished a second adrift of those ahead of him and will now start 18th, his worst grid slot of the year.
Behind him will be Lotus' Jarno Trulli and Timo Glock for Virgin, the latter sneaking under the 107% rule by 0.8secs.
However, for team-mate Jerome D'Amrosio and Hispania Racing duo Vitantonio Liuzzi and Daniel Ricciardo, their fate now rests in the hands of the stewards.
The trio will need to cite extenuating circumstances as to why they should compete, and they will likely point to the conditions as one of the factors.
Schumacher is in a similar position, but as he was competitive in practice, one of the factors upon which the stewards base their decision, it appears certain he will start, albeit at the back of the grid.
After claiming Red Bull's 13th successive pole, Vettel said: "It was a difficult session, with Q1 and Q2 very tricky, but with the circuit drying very quickly.
"However, I rediscovered Spa, found some better lines, and in Q3 I pushed on the last lap as hard as I could.
"With Lewis just in front of me I saw him locking up at the final turn and the last thing I wanted to do was lock up as well.
"But I'm very happy, and although they say it's going to be dry for the race tomorrow [Sunday], here you can never be sure."
Hamilton, in assessing his incident with Maldonado, was relatively restrained with his views, aware he would be called to visit the stewards.
"I was at the end of my Q2 lap, with a Williams going very slow in front of me, and I had to squeeze past," said Hamilton.
"After that I exited turn one and I saw Maldonado come up behind me quite quickly, and as he passed he swiped across me.
"There should never be an incident once the red lights are on (to signal the end of the session), but unfortunately there was.
"The front wing was quite badly damaged, and I thought the front suspension too, but the guys did a great job of putting the car back together and getting me out again."
Webber admitted to going "a bit too hard" early in the Q3, adding: "I probably could have built up a bit slower going into the third and fourth lap.
"We've had a smooth weekend, and it's easy to end up like JB (Button) and out of position, but we're in the hunt."
As for Button, he claimed what happened with his team was "a misunderstanding".
He said: "I did my first lap and then cooled the tyres not knowing I didn't have any laps left.
"I was second quickest when I did my lap, and then I didn't get another chance.
"Wow! That is massively disappointing and a huge shock. A big mistake on our part.
"In every practice session we've been in top three, so it's tough being back in 13th, but we've got to deal with it."