The 43-year-old has lost his seat for 2013 to Lewis Hamilton, and with a limited range of options available for him to stay in F1, he has opted to walk away, announcing his decision on the eve of this weekend's Japanese Grand Prix meeting.
While the partnership of Brawn and Schumacher was not the success either would have wanted during his comeback with Mercedes - the German only managed one podium in three seasons - their previous alliances at Benetton and Ferrari rewrote the record books.
Schumacher took seven titles and the majority of his 91 race wins while working with Brawn, and they formed part of Ferrari's 'Dream Team', along with Rory Byrne, Jean Todt and Paolo Martinelli.
They ended the Prancing Horse's 21-year wait for a drivers' championship success in 2000, and followed that up with further crowns in 2001, 2002, 2003 and 2004.
Schumacher initially retired at the end of 2006, but was convinced to make a comeback with the Mercedes team in 2010 by close friend Brawn.
However, his return to the sport he once ruled has not been a success and his only top-three finish with Mercedes came at Valencia earlier this year.
There had been suggestions Schumacher would join Sauber, for whom he raced sportscars in the late 1980s and early 1990s, in 2013, but he has instead opted to stop racing.
But Brawn has no doubt of the place Schumacher holds in the annals of Formula One history.
He said: "I think he is the greatest racing driver of this century and I was very privileged to work with Michael, we had some fantastic times, some tough times, but also some very successful times.
"Michael brought a lot to the team in his second period in the sport that people don't see.
"We haven't achieved what we wanted to achieve but what we achieve in future, Michael will have made a contribution to it.
"For me personally he is the greatest racing driver of this century."
Schumacher's voice broke with emotion as he revealed he would stop racing at the end of the season, but he insisted the decision to once again leave the sport was the right one, confessing he was "empty".
"It's not painful," he said. "It is a relief to me, I have done so much in this sport but when the battery is going low the first time, and then it is doing so again, and I am older, it is something I am looking forward to.
"There are plenty of other things in life you can do and now is the time to change that."
It seemed almost fitting that Schumacher should announce his retirement at Suzuka, a track where he has won six times, and where he clinched two of his titles, including the 2000 success that kick-started Ferrari's period of domination.
And he intends to finish his career on a high, starting with this Sunday's race in Japan.
He said: "It is now key what comes with the next six races to go. I will do exactly as I did the first time I retired, I will focus 100 per cent on what I am doing and then look at what happens next.
"I have options obviously but what they are I will decide when the time is right, I had options to stay but did not feel right about it."