Pole-sitter Sebastian Vettel and Ferrari duo Felipe Massa and Fernando Alonso came in for a fresh set of intermediate tyres in the final phase of qualifying on Saturday, all three clocking faster times than Lewis Hamilton on a drying track.
Brawn opted to keep Hamilton and team mate Nico Rosberg (sixth) on an older set of tyres, believing it was difficult to decide whether an advantage would have been gained with a fresher set in the dying minutes.
"It was a close call in our view and of course you may look silly if it doesn't work and you can't reverse out of it," Brawn told reporters.
"I think that this afternoon demonstrated that it (fresh tyres) was a stronger call but there's no easy or clear rules that you can use to come to that conclusion," added the Briton.
"We considered it before the session started and we had seen indications that the intermediates improved as they wore down but that doesn't seem to be the case."
Rosberg had been the fastest car on the track during the second phase of qualifying but a tropical downpour forced a change of strategy and denied Brawn the chance of knowing how quick the Mercedes is in ideal conditions.
"I don't think we were able to see the full potential of every car in the dry," he added.
"We certainly feel we are top six in terms of our cars so its a measure of where we are right now that we qualified fourth and sixth.
"Those places would have been very welcome last year, so its nice to see that this year we are disappointed."
Hamilton and Rosberg agreed that the car had been making rapid progress since the season began in Melbourne last week and were both looking forward to Sunday's second round of the championship.
"I am excited for the race. On the second row we have a good chance and we have worked very hard this week to get the long run pace set up nicely," Hamilton said.
"So if it's dry tomorrow we are in a good position to fight with the guys in front, if its wet, then the car's pretty good in the wet as well. Of course we want to go forwards... that's the plan."
Rosberg was hoping to emulate Kiki Raikkonen's win in the championship opener last week in Melbourne from seventh on the grid.
"Forwards is the way I want to go too. Raikkonen won from seventh last week and I am sixth, so everything is possible from my grid position."