The report by RFU chief disciplinary officer Jeff Blackett said Thomas had leaked confidential information to the media to undermine chief executive Steele, who left following a vote of no confidence.
A subsequent report by lawyer Charles Flint found there was no solid evidence to support Blackett's conclusions.
On Monday the RFU issued a statement on its website apologising to Thomas.
"The RFU now accepts that there was insufficient evidence to support these conclusions. Consequently, the RFU believes it right that these conclusions be withdrawn," the statement said.
"The RFU therefore apologises to Martyn Thomas."
Thomas stepped down from his role of acting CEO in November following the Flint investigation.
- Charles Flint