The shock departure of Flamengo's biggest idol highlights the crisis at the Brazilian champions, under their third coach of the year and languishing in 15th place, three points above the relegation zone.
About 100 fans held a demonstration outside Flamengo's Rio headquarters with banners in support of Zico, who accused rival members within the club of sabotaging his work.
One fans was held in custody by police after throwing a rocket at the Flamengo gates, media reported.
"It's not possible to do what I want with Flamengo," said Zico, who is considered one of Brazil's greatest players and was executive director of football at the club.
"I've noticed that my presence has not been favourable and has caused discontent among a lot of people," Zico added in a statement posted on his website on Friday. "It's not possible for me to continue."
Before Friday's practice, held behind closed doors, Zico visited Flamengo's training grounds to say goodbye to the players and club president Patricia Amorim.
He left his beloved club without speaking to reporters but Patricia summed up the squad's feelings.
"My heart's broken. Our project for the future has been set back, now we need to stabilise the present," she told reporters. "He is big and strong, that's why he's Zico."
POPULAR RETURN
Zico, whose return to Flamengo this year was greeted by fans as a great signing, said his opponents had been criticising his sons to get at him.
"I've been unfairly attacked, mainly via my sons, who have not been involved at any time, and this goes against the values and concepts I learned with my father.
"I can't allow this cowardly feud to continue using my family.
"Today, my grandson Antonio was born but Flamengo died in my heart," added Zico, who coached Japan at the 2006 World Cup and led Fenerbahce to the Champions League quarter-finals in 2008.
During Zico's short return to the club, Rogerio Lourenco was sacked as coach and replaced by former Brazil midfielder Silas, who himself is now in danger of being fired.
The team, with only one win in their last 12 matches, face Botafogo in their Rio derby on Saturday and anything other than a victory could seal Silas's fate.
Zico is the most popular player the club has produced, having played in a golden generation which won three Brazilian championship titles, the South American Libertadores Cup and the World Club Cup.
Flamengo claim to have 25 million supporters in Brazil but the club is notorious for its political in-fighting as well as the enormous pressure placed on coaches and players.
