Warner, 68, who had been suspended pending a FIFA Ethics Committee probe into bribery claims, has resigned from all his international football posts including the position of CONCACAF president.
"FIFA regrets the turn of events that have led to Mr Warner's decision," the organisation said in a statement.
"As a consequence of Mr Warner's self-determined resignation all ethics committee procedures against him have been closed and the presumption of innocence is maintained."
Warner was being investigated in a cash-for-votes scandal relating to the campaign of then-FIFA presidential candidate Mohamed Bin Hammam that rocked football's governing body in the run-up to the June 1 election.
At the centre of the investigation was a meeting with Caribbean Football Union (CFU) members in Trinidad relating to Bin Hammam's campaign which was organised by Warner and the Qatari.
"This decision [to resign]... comes during the sequel to the contentious Mohamed Bin Hammam meeting in Port of Spain in May with CFU delegates," Warner said in a statement.
"I am convinced, and I am advised by counsel, that since my actions did not extend beyond facilitating the meeting that gave Mr. Bin Hammam an opportunity to pursue his aborted bid for the FIFA presidency, I would be fully exonerated by any objective arbiter.
"I have, nonetheless, arrived at the decision to withdraw from FIFA affairs in order to spare FIFA, CONCACAF and, in particular, CFU and its membership, from further acrimony and divisiveness arising from this and related issues."
Bin Hammam quit the race for the presidency shortly before being suspended in late May along with Warner, paving the way for Sepp Blatter to be re-elected unopposed for a fourth term with an immediate pledge to beef up the fight against corruption.
Warner was until recently an ally of Blatter for the near 30 years. The Trinidadian was involved with FIFA and CONCACAF, the North and Central American and Caribbean football confederation.
FIFA observers say Blatter gave him a free hand to run CONCACAF as he saw fit in return for the block support of its 35-member federations.
However, last month Warner threatened to unleash a "football tsunami" by revealing contents of emails with Blatter before later backing down for what he said were legal reasons.
POLITICAL CAREER
An angry Warner made public an email sent by FIFA Secretary General Jerome Valcke that suggested the 2022 World Cup was "bought" by Qatar.
Valcke later said he meant the bid had used its financial strength to lobby for support.
Warner was re-elected unopposed as CONCACAF president in May before some supporters turned against him after his ban.
He and Bin Hammam had been accused of attempting to bribe delegates of the Caribbean Football Union with inducements of $40,000 to vote for the Qatari.
Warner, who has denied any involvement in bribing or attempting to bribe delegates, will now focus his attention on his political career in his home country.
"I shall, henceforth, be concentrating exclusively on my lifelong commitment to the service of the people of Trinidad and Tobago, currently as chairman of the major party in our governing coalition and as a cabinet minister in the government of our republic," Warner said.
FIFA said his resignation had been accepted and said his "contribution to international football and to Caribbean football in particular and the CONCACAF confederation are appreciated and acknowledged."
CONCACAF is currently staging the Gold Cup continental championship in the United State
