The airline had previously grounded its domestic and regional routes on 21 June, after being served with a suspension order by the Nigerian Civil Aviation Authority (NCAA).
A spokesperson for Gatwick says Air Nigeria has "no further flights planned" to the UK airport.
"The last service was on Sunday [9 September] and Air Nigeria has now suspended operations," she says, adding that reports of passengers being asked to contribute money for fuel payments were "hearsay".
Air Nigeria chairman Jimoh Ibrahim is quoted by Reuters as saying that the carrier aims to resume operations in 2013.
"Corporations are like individuals, who naturally will get sick, and the usual thing to do is to admit them to hospitals, either for corporate surgery or for treatment, as the case may be," he says in a statement obtained by the newswire.
The airline has suffered a number of regulatory and financial setbacks in recent weeks.
In addition to two NCAA suspension orders - issued on safety grounds in the wake of the Dana Air Flight 992 crash - Nigeria's Federal Inland Revenue Service (FIRS) had launched an investigation into the company's tax arrangements.
Air Nigeria operated the Gatwick route with an Airbus A330 wet-leased from EgyptAir (registration SU-GCI). Plans to receive a second EgyptAir A330 (registration SU-GCJ) were put on ice.
The carrier's management team had voiced optimism of overturning the NCAA suspension order, and were planning to add Johannesburg, Paris and Rome to its international network.
Air Nigeria started life as Virgin Nigeria in 2004, following an agreement between Nigeria's government and the Virgin Group.
After being rebranded Nigerian Eagle Airlines in 2009, Virgin Atlantic Airways sold its 49% stake in 2010 and the airline became Air Nigeria under new majority shareholder and chairman Jimoh Ibrahim.
An Air Nigeria spokesperson did not immediately respond to a request for comment.
