His son Mick, who represents Haas, was unable to attend due to illness, but Schumacher's wife Corinna, 53, and daughter Gina-Maria, 25, were present to accept the honour on his behalf, joined on stage by Todt.
Those in attendance at the ceremony paid tribute to Schumacher with a standing ovation, and the touching gesture led to Corinna breaking down in tears in what was an incredibly poignant moment.
After the event, Todt tweeted: "An emotional ceremony in Cologne to honour Michael Schumacher's outstanding career and charitable streak with Corinna, Gina, Mick Schumacher and Henrik Wust.
"I met Michael 30 years ago, with Ferrari, living his passion and bringing joy to millions of us!"
Reacting to the standing ovation, Todt later told Bild: "That's just natural. No one planned it to be so emotional that tears were shed by Corinna, but sometimes it's good to not always control yourself."
Earlier this week, Todt gave a rare insight into the seven-time F1 world champion's condition in an interview with German TV channel RTL.
"I don't miss Michael, I see him," he said.
"Yes, it's true, I watch races with Michael. But sure, I guess what I miss is what we used to do together."
Corinna has been fiercely protective of her husband since the accident and revealed how the family have dealt with the traumatic situation over the past nine years.
"Michael is here. Different, but he's here, and that gives us strength, I find," Corinna told Netflix documentary SCHUMACHER.
"We're together. We live together at home. We do therapy. We do everything we can to make Michael better and to make sure he's comfortable. And to simply make him feel our family, our bond.
"And no matter what, I will do everything I can. We all will.
"We're trying to carry on as a family, the way Michael liked it and still does. And we are getting on with our lives.
"'Private is private', as he always said. It's very important to me that he can continue to enjoy his private life as much as possible.
"Michael always protected us and now we are protecting Michael."
