Cameroon, who were originally scheduled to stage the 2019 tournament before being stripped of hosting rights, entered the competition as defending champions.
They came second in their group behind Ghana and allowed Nigeria to come from 2-1 down to win their last 16 tie 3-2.
Patrick Kluivert, Seedorf’s assistant and former Netherlands international teammate, was also dismissed.
The pair had come under fire during the tournament for constantly changing the formation.
After the Nigeria defeat, Seedorf, who took up his role in August 2018, said he was happy to continue as coach.
However, the federation issued a statement terminating the four-year deal. “Following the premature exit of Cameroon's men's flagship squad, Cameroon's football federation, in line with clauses in their respective contracts, has decided to bring an end to the contracts of Seedorf and Kluivert.”
Seedorf, 43, enjoyed a trophy drenched career as a savvy midfielder at Ajax, AC Milan and Real Madrid.
However he has stuttered as a coach. He has been sacked from posts at Milan as well as Shenzhen in China. He was at the helm when Deportivo La Coruna were relegated from the Spanish top flight in April 2018.
Deportivo started the campaign with Pepe Mel as manager. They then hired Cristóbal Parralo in October 2017 before drafting in Seedorf in March 2018.