McInnes and assistant Tony Docherty led Saints to the First Division title and comfortable safety in their first season in the Scottish Premier League before departing for Bristol City in October 2011.
Saints have continued to progress since then with Steve Lomas guiding them to Europa League qualification in consecutive seasons before Tommy Wright stepped up when his fellow Northern Irishman left for Millwall.
McInnes said: "There have been a few changes and there have been two different managers but the nucleus of the team is still there.
"It's a good story, St Johnstone. When I left we were sitting in fourth position and I always felt we would get into the top six that season.
"To compete in Europe for the last two seasons is brilliant for them.
"The players are happy there and that says a lot for the club. They have a really good loyal support and they were always good to me.
"I'm pleased for everyone connected with the club. They have shown what can be done when a club is run properly, when the right standards are set on and off the park.
"Steve and Tommy will never have had to crack the whip with those boys, they are proper good professionals.
"The nucleus of that team will be running that dressing room now and both managers have done well with that group of boys, and I'm not surprised in the slightest."
Saints have had contrasting fortunes in recent weeks - beating Ross County 4-0 before losing by the same scoreline to Dundee United.
But neither McInnes or Wright are reading too much into the Tannadice score.
McInnes said: "St Johnstone ordinarily don't lose a lot of goals. They very rarely lose by that margin. So everyone was shocked by the result last week, and I think it's a one-off for them.
"They are always very difficult opponents, very resolute and always a very committed and organised side."
Wright said: "We have analysed it and we are not going to get too downbeat about it because on reflection we actually played quite well in the game.
"We probably got into the final third more times than Dundee United did but they made more use of their chances."