Stoner, a two-time champion, announced on Thursday ahead of the French Grand Prix that he will leave the championship at the end of the 2012 season.
The Honda rider, 26, is the reigning champion and the current points' leader.
Ducati rival Rossi believes Stoner's loss is a big shame for MotoGP.
"I think it's most of all a negative thing for MotoGP, because we are losing the reigning world champion and current points leader, so from a technical point of view the series is losing out a lot," Rossi told reporters at Le Mans.
Rossi, enduring one of his worst starts to a season with Ducati, denied he himself was thinking about quitting the sport, although he admitted he had thought about the possibility in the past.
"Yes, but I will tell you I'm not retiring, and then I'll retire without doing this, because I don't love goodbyes much," he added.
"You will know when I'm at home already! Joking apart, for a rider it can be an unforgettable moment, but perhaps more for the wrong reasons rather than the good ones.
"It's sad, because you'll have to think about changing your lifestyle and to abandon what you have been doing for perhaps 15 years, so it's something you surely won't forget."