Jones was dropped more than a week ago by the Australian Rugby Union but Gregan remained tight-lipped for several days before finally commenting on the decision at a lunch to name the Rugby Union Players' Association's Rugby Medal for Excellence winner.
"We've gone through a lot together," Gregan said.
"We've had our ups and our downs but it's been a very good working relationship. I spoke to Eddie on the day - I don't really need to debate this publicly.
"He knows how I feel about it. He's been a big part of my life and career since 1998," Gregan added, after the pair worked together with the ACT Brumbies before Jones took over the top job in 2001.
"He'll do really well in whatever he chooses to do in the future.
"It (the sacking) is the nature of what we do. We are judged on results. It's got no reflection on his work ethic. It's outstanding. It's just disappointing we didn't get the results. The coach particularly is always under pressure."
Gregan would not be drawn on his own future however, saying only that he plans to concentrate on next year's Super 14 with the Brumbies before turning his attention to his international standing when that tournament is over.