German football association (DFB) president Wolfgang Niersbach welcomed the move and said he could not understand why FIFA had taken such a drastic step in the first place against someone who had done so much for international football.
Beckenbauer, one of the world's best known former players, had been banned two weeks ago after refusing to cooperate with an investigation into the award of the 2022 World Cup to Qatar.
The 68-year-old is a former member of the FIFA executive committee which controversially awarded the World Cup to Qatar in 2010, and had received "repeated requests" to provide information, FIFA said in a statement at the time of the ban.
Beckenbauer has since had a change of heart and offered to provide responses to the questions which he had initially rejected because they were written in "legalese English."
FIFA Secretary General Jerome Valcke told reporters that Beckenbauer could now attend the tournament he graced as a player with West Germany.
Beckenbauer has however indicated he has no plans to come to Brazil for the tournament.
"As you know Franz is someone we all respect and was an amazing footballer and we would love him to have him here at the World Cup, even more because his national team is playing in the second round," Valcke told reporters in Rio de Janeiro.
"But it is his decision not to come to Brazil and that's his decision," he added.
"OVER REACTION"
Beckenbauer's manager Markus Hoefl had earlier announced the end of the ban, saying it had been unjust but conceding that it would have been better had the former player answered the questions posed to him by the commission earlier.
"I underestimated the situation mainly because such issues were usually dealt with by my management," Beckenbauer said.
The ban issued at the start of the World Cup in Brazil meant he could not attend any games in an official capacity, embarrassing such a high profile figure in the game.
FIFA told Beckenbauer that a repeat of his actions could lead to further sanctions.
DFB president Niersbach said FIFA's ban was an over-reaction.
"It was completely incomprehensible to me why such a ban was issued on the second day of a World Cup," Niersbach said in an emailed statement to Reuters.
"Perhaps Franz made a formal mistake but still that's not the proper way to treat someone who has done so much for football all around the world."
As a player, Beckenbauer redefined the role of libero or sweeper and captained the West Germany side which won the 1974 World Cup.
He led West Germany to World Cup victory as a coach in 1990 and was head of the local organising committee when Germany hosted the showpiece in 2006.
(Reporting by Karolos Grohmann and Erik Kirschbaum; editing by Keith Weir)
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