Rosberg's car reverted to a standard exhaust rather than the Coanda effect system used since the Singapore GP in September.
While he could only manage 17th, his team-mate Michael Schumacher was sixth in the latest car.
Rosberg said he had been content to follow the team's strategy and was taken aback by his lack of qualifying speed.
"We tried our car from four months ago, practically," he said.
"On Friday we tried it, but not for one lap, on a long run. And on a long run it looked good, not too far off Michael's car.
"But then this morning I was in our current car and we decided 'let's give it a go' and for qualifying changed to the older version because it wouldn't be too different and maybe there was something we could learn.
"So we did that and it put me much further back than expected. It's very, very surprising to lose that much performance."
Team boss Ross Brawn said the speed deficit was exacerbated by Rosberg's car failing to generate tyre temperature.
"What became critical was getting the tyres warm," Brawn conceded.
"Every car had to do quite a lot of laps to get the tyres warm, and with Nico we just fell off that edge with getting the tyres hot enough."
Rosberg insisted the move was still useful even though it compromised his weekend.
"The positive is that we learned something. And also that if you look at what Michael did and what I did, it proves we're doing well on development and we are moving forward quickly," he said.
Brawn also defended the strategy, saying 2012 results are less important to Mercedes than rebounding properly in 2013.
"I think the stuff we're doing with Nico is all very important stuff for next year," he said.
"Our priority now is to make sure we go into the winter with as clear an understanding as we can of how the tyres work and how the car's working so we can come out next year in a much stronger position."
Despite his lack of qualifying pace, Rosberg remained hopeful of a better race.
"One of the reasons we did it was hoping that the race pace would be better, so maybe tomorrow I can be very strong," he said.
"It didn't feel like it today, but you never know."
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