Frenchman Romain Grosjean was fourth fastest while Venezuelan Pastor Maldonado was eighth at the high-speed circuit.
Grosjean will drop five places, however, for an unscheduled gearbox change which will lift Maldonado up to seventh.
The grid position provided a rare ray of sunshine for a team whose weekend has been clouded by the threat of having their cars impounded after Sunday's race.
Former French reserve driver Charles Pic has taken action against the team, saying they failed to give him the track time he paid for last year.
The case has gone to arbitration but Pic has secured a Belgian court order effectively preventing Lotus from removing their cars from the circuit.
"They have not respected the contract," he told France's Le'Equipe newspaper. "It's not just about the number of days in the car but other aspects I prefer not to elaborate on."
Lotus co-owner Gerard Lopez, who was not present in Spa, told autosport.com that he was confident the matter would be resolved.
"We are having our legal department look at it. This will be solved and solved in a manner that is adequate," he said.
"I know we'll find an amicable solution and the show goes on. I think the cars will leave as planned. I don't envisage there being an issue. I know there will be a resolution."
Lotus, previously the title-winning Benetton and Renault outfit, faced a winding-up petition brought by creditors last month but the matter was resolved out of court.
At the Hungarian Grand Prix, the team blamed a banking hitch for a delay in Pirelli releasing tyres to them ahead of first practice.
Asked about the situation at the team, Formula One supremo Bernie Ecclestone had limited sympathy.
"I think they’ve been in problems for quite a while. So this is a good place for somebody to start an action," he told Reuters on Saturday.
"People should pay their bills, shouldn’t they? That’s my position always. If they owe some money they should pay it. it shouldn’t be necessary to have this happen."
(Editing by Tony Jimenez)
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