The appeal by his lawyers was lodged late last night, a day after the Home Office believed the deadline expired.
An appeal 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 had already said the process could take months.
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, believing the deadline for an appeal had passed, said he could be removed from the UK "in full compliance of law".
When the row over Abu Qatada blew up three months ago, ministers said very little publicly about the case knowing very well that their Labour predecessors had promised a deportation that never came.
Tuesday's statement by Theresa May was pretty clear: the process was back on track and the cleric could be gone in months.
When Strasbourg halted the deportation on 17 January, the parties were told they had three months to request an appeal to the Grand Chamber.
The court insists the deadline was midnight Tuesday on.
If the Home Office is wrong, Strasbourg's confirmation of a last-minute appeal is a shattering development. But the Home Office insists that it circled the right date on the calendar.
Any case that has a full hearing in the Grand Chamber can take a year to resolve. The renewed deportation attempt begun on Tuesday would grind to a halt.
However, on Wednesday the court said it received a request at 23:00 BST on Tuesday - before the deadline expired.
When the appeal was revealed, a Home Office spokesman denied that it had made a mistake about timing, saying the European Court was "wrong".
A spokesman said that Abu Qatada had "no right to request to refer the case to the Grand Chamber [of the court] because the three-month deadline passed at midnight on Monday".
He said the government was writing to the European Court to make the point that the case should not be referred because the deadline had lapsed.
He said the government would resume the deportation process when a decision on referral was made and would oppose any request for bail.
If the judges decide the case will not go before the Grand Chamber, the deportation process can resume.
Blocked deportation 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.
Weeks later, his six-year detention in the UK ended on the orders of a judge, under strict bail conditions, including a 22-hour curfew allowing him to leave home for a maximum of an hour, twice a day.
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We want the home secretary to go through the proper processes, abide by the law so we don't end up having to pay compensation to this ghastly man”
Chris Bryant Shadow justice minister 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.
BBC political correspondent Norman Smith said if the deadline was indeed Tuesday it would raise the issue of whether Abu Qatada had been arrested and detained before UK officials were legally entitled to.
Keith Vaz, chairman of the home affairs select committee, said the situation had turned "chaotic and almost farcical".
"It's very important that [Mrs May] should clarify this as soon as possible by making a statement to the House after she knows what the facts are," he said.
Conservative MP David Ruffley said Mrs May "had been frustrated, through no fault of her own, by this appeal".
Shadow justice minister Chris Bryant said Mrs May had failed to check all the relevant details in the run-up to Abu Qatada's arrest.
"All of us want Abu Qatada to be deported to Jordan; we also want the home secretary to go through the proper processes, abide by the law so we don't end up having to pay compensation to this ghastly man - but what seems to have happened is that the very basic, details weren't done before the big fanfare of the announcement yesterday."
