Horwill, 28, was cited for allegedly stamping or trampling on Lions counterpart Alun-Wyn Jones early in the match at Lang Park, which the hosts lost 23-21, but was cleared by judicial officer Nigel Hampton who found the contact to be accidental.
"The International Rugby Board has confirmed to the Australian Rugby Union that it will appeal the James Horwill disciplinary decision following an extensive review of the case," the governing body said in a statement on Thursday.
"... given its duty to preserve player welfare at all levels of the game, the IRB is compelled to further examine potential acts of foul play which either potentially or in reality impact on the preservation of player welfare.
"It is important for the IRB to ensure amongst all stakeholders in the game that there is full confidence that priority is given to player welfare and the values of the game."
The appeal will be heard following Saturday's second test and Horwill is free to play pending the outcome, the IRB added.
The Australian Rugby Union (ARU) said it was "surprised and disappointed" by the IRB's decision to re-open the case.
"This is an unprecedented step taken by the IRB in what is the most important rugby event staged in Australia since the 2003 Rugby World Cup," ARU chief executive Bill Pulver said in a statement.
"While we respect the right of the IRB to intervene, we also respect the knowledge and experience of appointed - and independent - judicial officers, and their expertise to consider evidence and reach sound findings.
"James Horwill was cleared of the stamping charge as per the IRB's established judicial process. We are surprised and disappointed that the finding of Mr Hampton is now not only under question but deemed to be 'erroneous'."