Farrell, who has had several suspensions related to tackle technique in his career, was expected to receive a minimum four-game suspension for the act of foul play.
The appeal will be heard early next week, Six Nations Rugby said, with Farrell left out of England's matchday squad for their World Cup warm-up Test in Ireland on Saturday.
He was surprisingly let off the hook by the Judicial Committee on Wednesday, who agreed with the flyhalf that the offence warranted a yellow card only.
Farrell was sent off - a yellow card upgraded to red via the new review system - after smashing his shoulder into the face of Wales forward Taine Basham in the sort of no-arms tackle that got him a four-game ban this season playing for Saracens.
The Judicial Committee decision caused uproar on social media, with ex-players and player welfare advocates almost unanimous in agreeing it set a bad example at a time when the long-term effect of head injuries is in the spotlight.
"World Rugby has today confirmed to the Rugby Football Union and Six Nations Rugby that it will exercise its right to appeal in regard to the Owen Farrell disciplinary decision following a careful review of the independent Judicial Committee's full written decision received on 16 August," World Rugby said.
"Having considered the full written decision, World Rugby considers an appeal to be warranted. In line with provisions set out under Regulation 17, an independent Appeal Committee will be appointed to determine the matter at the earliest possible opportunity."
The statement added that while World Rugby "fully supports the important role that an independent disciplinary process plays in upholding the integrity and values of the sport", it is clear they too believe the judgement sends the wrong message. "Player welfare is the sport's number one priority, and the Head Contact Process is central to that mission at the elite level of the sport," it continued.
Any suspension Farrell receives could potentially see him miss a number of England's World Cup pool matches.
They have two more warm-ups against Ireland and Fiji, with their first two World Cup games against Argentina and Japan crucial for Steve Borthwick's side.
Samoa and Chile are also in their group.Â
