Jenson Button led the World Championship entering the Belgian race weekend despite not scoring a podium since early June.
The respective recoveries of Ferrari and McLaren ensured that the last two World Champions, Kimi Räikkönen and Lewis Hamilton, had scored podiums in the two races leading up to Belgium.
Force India's Giancarlo Fisichella posted the fastest time off the wet runners followed by Nico Rosberg.
Badoer qualified 20th for the second race in a row, after crashing at the end of the session and bringing out the yellow flag, causing many drivers to slow down.
The other four drivers to be knocked out at the end of the session were Renault's Romain Grosjean (P19), Williams's Kazuki Nakajima (P18) and the two Toro Rossos of Jaime Alguersuari (P17) and Sébastien Buemi (P16).
The session was topped by the Toyota of Jarno Trulli, while BMW Sauber's Robert Kubica was second with Red Bull's Vettel coming third.
The two McLarens of Heikki Kovalainen (P15) and Hamilton (P12) were also knocked out along with the second Renault of Alonso (P13) and Force India's Adrian Sutil (P11).
The two BMW Saubers' new updates seemed to be lifting the whole team as Kubica (P5) and Heidfeld (P3) achieved their best qualifying positions of the season.
Lewis Hamilton backed off after seeing the incidents ahead of him, which caused Jaime Alguersuari to run into him; both crashed into the barrier and retired.
Mark Webber was released in front of Nick Heidfeld and was handed a drive through penalty, severely affecting his race.
Fernando Alonso retired on lap 27 with a suspected wheel problem after a first corner collision with Adrian Sutil.
[10] Vettel recorded the fastest lap of the race with a late push to try to catch the leaders but it was to no avail as Räikkönen took the chequered flag for the first time this season with Fisichella scoring Force India's first-ever points with a second-place finish.
With Button failing to score, his championship lead became smaller for the second race in a row as his teammate Barrichello closed the gap by two points.
[12] On 31 August Force India team principal Vijay Mallya reported that Fisichella would not be driving for Ferrari at Monza.
[14] Force India announced on 7 September that Vitantonio Liuzzi, the team's test driver, would replace Fisichella for the remaining five races of the season.
[15] On 4 September, Renault were summoned to a meeting by Formula One's governing body, the FIA with the allegations of race fixing during the 2008 Singapore Grand Prix.