It was a happy development for Thomas, who had been out of baseball since leaving a similar post with the Milwaukee Brewers a few years earlier.
"I was getting bored. You can only go fishing with [former Cardinals manager] Whitey Herzog so much," Thomas said with a laugh. "You can only play golf so much. And I'm such a bad golfer that I didn't even want to play. I'm kind of an active guy and I like to do things. So I was really glad to get this opportunity, especially with Dan."
In the meantime, the Phils were winning five straight division titles. In that span, they won two pennants and a World Series championship. They've celebrated on the field and sprayed champagne in the clubhouse so many times that the memories sort of run together.
It wasn't always that way, of course. From 1983, when they lost to the Orioles in the World Series, to 2007, when they began their streak of National League East crowns, the Phillies made it to the postseason just once.
That was in 1993, when Thomas assembled a roster of spare parts and castoffs that electrified the city, upset the mighty Braves in the NL Championship Series and appeared to be on the way to taking it all before Joe Carter's home run against Mitch Williams in Game 6 popped the bubble.
What makes the accomplishment even more impressive is that the Phils in those days played in outmoded Veterans Stadium and had one of the lower payrolls in the Majors.
"That was a great feeling," Thomas recalled. "I'll always remember [manager Jim] Fregosi and [then team president] Bill Giles and myself riding around the field in a convertible there and holding the trophy up.
"Philly's a great baseball town. When you win, they really embrace you. And when you don't do what you're supposed to do, and I'm talking about non-hustling players, they let you know. So if you go to Philadelphia to play, you'd better give it 100 percent."
The magic of '93 didn't last. Catcher Darren Daulton hurt his knee. Center fielder Lenny Dykstra began having back problems. Neither was the same player again. Platoon left fielder Pete Incaviglia was unable to duplicate his production and the pattern was set. At the end of the 1997 season, Thomas was informed that the Phillies had decided to make a change.
Still, he'll always be grateful to Giles, who gave him his big break in the business, taking a chance on the Cardinals' farm director by naming him the Phils' general manager in the middle of the 1988 season.
Even the interview process was unusual. Thomas spent two nights at Giles' Main Line home. One evening they stayed up past 2 a.m. ET, talking baseball and playing pool.
"Then he said, 'Tomorrow, we're going to interview with some of our other people,'" Thomas said. "So I walked into his living room the next morning and there must have been 20 people there. Everybody in the organization, I think."
The two men developed a strong bond that remains to this day. At the same time, Thomas was growing close to Duquette, who was then the general manager of the Red Sox. Immediately after being let go by the Phillies, he was offered a job in Boston.
"He called me the next day and he said, 'Do you still want to work?'" Thomas said. "And I said, 'Sure.' He said, 'I've got a job for you.' I said, 'What do you want me to do?' He said, 'Well, let's talk about it. About anything you want.' So that was really great of him and I appreciated it."
It was a gesture that would be repeated years later.
Thomas stayed with Boston through the 2003 season, Theo Epstein's first year as general manager, and then spent three years working with Brewers GM Doug Melvin.
Thomas still has close friends in the Philadelphia area. He and his wife, Susie, strongly considered staying in the area even after he no longer worked for the Phils before moving back to St. Louis. And he'll always have 1993.
"I see Joe Carter bouncing around the bases in my nightmares," Thomas said, laughing again. "But what a great year that was. It was really neat."
Alumni Weekend (Aug. 2-4) will feature a salute to the 1993 NL champions. Thomas and many of his players will be there.
"I can't wait," he smiled.
Paul Hagen is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.