His tenure was ended by the serious shoulder injury which forced Petrie out of the 2005 autumn internationals.
The Glasgow Warriors skipper made his Scotland debut against New Zealand in 2000 and is to leave rugby for a new career in the energy sector.
He said: "Pro rugby has been my whole life for the past 10 years or so and is a difficult thing to let go of.
"I've had some fantastic times with Glasgow, and with Scotland, but I have a gut feeling that now is the right time to move on to something new.
"I'd like to thank everybody for the support that I've been given throughout my career, especially the fans here in Glasgow, who have always been great to me."
Hadden paid his own tribute to Dundee-born Petrie.
"I remember Bill McLaren coming to watch the Caledonian Reds training at Perth in '97 and he asked who the young fellow was," Hadden recalled.
"I told him it was Jon Petrie and he should remember the name because he was going to play for Scotland.
"This is not something I would normally do, which is why I remember it so clearly, but it was obvious to everyone that he was going to make a big impact.
"When I took over as Scotland coach, Jonny was my first choice as Captain and he did a great job, leading the team to a first ever win over the Barbarians at Pittodrie and only our second ever win in Romania.
"Latterly he has been dogged by injury but his excellent communication and leadership skills will stand him in good stead whatever career path he chooses."