Already facing a five-place grid penalty after a morning gearbox failure, the Mercedes driver was only 18th fastest at Spa.
Rosberg crossed the line moments too late to manage a last run in Q1, leaving him unable to respond after being pushed back outside the Q2 cut-off.
"It was definitely not good," said Rosberg.
"To start off with the gearbox this morning just makes it all the more difficult.
"Now a miscommunication, but it was probably more my fault. We just didn't get it right and that's it, 18th.
"But either way I don't think it would've changed all that much with a five-place grid penalty tomorrow.
"We need to do a good strategy tomorrow and we'll see if we can get some points, but it's going to be difficult."
Rosberg's team-mate Michael Schumacher was only 13th fastest.
"I felt rather excited seeing my laptimes because I pulled out more than we had expected to do, so it was a good lap," said Schumacher, who is taking part in his 300th grand prix weekend.
"I was hoping and waiting for the message that it was going to be enough. I was waiting longer and longer. I was hoping it was good news, but then when it came I was obviously rather disappointed."
Schumacher said the Mercedes was simply not quick enough at Spa.
"If you look at the middle sector we're losing 1.1 seconds," he said.
"In the first and last sector we're losing about two tenths in each of them.
"So we're much too slow in the middle sector. Generally if a car is not competitive that's where you lack the pace."