Lee and fellow South Korean player Kim Ki-jung are eligible to resume competition immediately after the Malaysia-based BWF found that the "whereabouts failures" were due to the management of the program by the national badminton federation.
Neither player failed a doping test, but had been required to provide whereabouts information for the BWF to conduct out-of-competition testing.
Lee and Kim accumulated three "whereabouts failures" in 2013 and received the ban in January, despite a disciplinary panel finding that there were extenuating circumstances because the Badminton Korea Association failed to "make diligent efforts to keep the BWF informed about the players' whereabouts."
The BWF on Tuesday announced it had reversed the ban "based on significant new evidence" presented in a subsequent disciplinary process against the BKA.
The disciplinary "panel has determined all strikes for missed tests and filing failures against both players in 2013 are cancelled and that no violation was therefore committed," the BWF statement said.
The BKA was fined $41,170 for failing in its duty of care for Kim and Lee through administrative failures in the management of the whereabouts system which contributed to the three strikes against them.
Lee won gold in the mixed doubles at the 2008 Olympics and bronze in the men's doubles at London 2012.