The appeal was lodged just before the deadline last night.
This means the deportation process cannot begin until a panel of judges has decided whether the case should go to the Grand Chamber of the court.
Home Secretary Theresa May acknowledged on Tuesday that the process could take months if an appeal were started.
Abu Qatada, 51, who faces charges in Jordan of plotting bomb attacks, had been arrested on Tuesday and denied bail.
In a statement to the Commons later, Mrs May said he could be removed from the UK "in full compliance of law".
The last-minute lodging of the appeal by his lawyers was a huge embarrassment and blow to Mrs May, says BBC correspondent Danny Shaw.
The European Court of Human Rights had blocked Abu Qatada's deportation to Jordan in January, saying evidence obtained by torture might be used against him.
Mrs May travelled to Jordan in March for talks with the king and ministers on the case of the Palestinian-Jordanian, whom ministers have described as "extremely dangerous" and consider a threat to UK national security.
Before the appeal was lodged, lawyers for Mrs May had told a Special Immigration Appeals Commission hearing this week that she intended to deport the cleric on or around 30 April.
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