The Briton failed to make Q3 for the first time since the 2010 Malaysian Grand Prix, finishing down in 12th position after saying he had driven like an 'idiot'.
Brawn revealed afterwards that Hamilton had damaged his car's floor earlier in the session, and was losing performance as a result.
He said the team found the problem too late to fix it.
"Lewis was looking OK, but unfortunately he hit a kerb and damaged the car's floor," Brawn said after qualifying.
"We didn't realise the consequences of that until a bit later in the session.
"It was irreparable, so that was unfortunate as well. It just wasn't our day. We have to try to do a better job."
Brawn admitted it had been a poor day for Mercedes after Nico Rosberg had been hindered by a problem in Saturday morning's practice session.
"It definitely wasn't a great day for all of us today," he added.
"We had a reliability issue with Nico in the morning, which meant we lost most of the session, and to me Monza is always about confidence for the driver.
"I think losing that amount of time was always going to be difficult and it meant we didn't really have a great balance on Nico's car during qualifying. That wasn't great."