World No 1 Djokovic is chairman of the player council and he led a revolt against ATP chairman Chris Kermode, who will step down at the end of the year.
The majority of the top ATP stars were agains the removal of Kermode.
Djokovic also came under fire for backing the controversial Justin Gimelstob after he pleaded no charge to a battery case.
Jamie Murray, Robin Haase and Sergiy Stakhovsky all resigned from the player council because they were unhappy with a number of decisions.
But Federer and Nadal, along with Jurgen Melzer, have stepped up to challenge Djokovic and they are determined to do good for the sport.
“We (he and Federer) decided to be together out there,” Nadal said.
“I will not be alone there. He will not be alone there.
“Both of us can [combine to] be a good power, good help for the sport in some way — hopefully in a better way.
“We are here to help and to know a little bit better what’s going on. Last year have been some up and downs in a lot of things.”
“[There have been some] tough moments in terms of discussions — a lot of important things to have to be done.
“I will try and give my opinion after more than 15 years on the tour. I can probably give a different perspective on how the game has to be or things that we can add.
“It’s just trying to help the game to be better. If I am there, I believe that I can be helpful.”
Meanwhile, Murray praised Nadal and Federer for replacing him in the council.
“Massive shout out to Roger Federer and Rafael Nadal for stepping up to join the ATP player council,” he wrote on Twitter.
“Despite the sports current success we live in chaotic times.
“My biggest achievement on the council may well prove to be being part of the group of resignations that presented the opportunity for this to happen.
“Good luck!!!”