Club president Peter Siemsen announced the decision at a news conference on Monday saying 'Flu' needed a breath of fresh air and would take their time to find a suitable replacement.
"It worked for two years but now it's not working," Siemsen said of Abel's leadership since he took charge in 2011.
An emotional Abel, who was given a miniature of the championship trophy as a memento, said he understood the club's decision and would have done the same.
"If I was a director I also would have changed coach. Thank you all, without exception... for giving me these moments. They were 26 months, something rare in Brazilian football," Abel said of the time he had in charge in his second stint at Fluminense in a volatile league in which coaches seldom last more than one season.
Rio-based Fluminense are at home to leaders Cruzeiro at the Maracana on Wednesday with the club's under-17 coach Marcos Valadares likely to be in charge of the first team.