The device was made safe by officers in the Derrylin Road area at around 11am on Saturday, following a major security operation which began in the early hours of Friday.
A number of local homes had to be evacuated overnight.
The army carried out a clearance operation centred on a suspicious Silver Volkswagen Bora car along the rural road close to Enniskillen.
Inside it they discovered a beer keg containing 60kg of homemade explosives, which could have "killed or seriously injured".
Police said early investigations suggest the car bomb was destined for Lisnaskea PSNI station.
In a statement, District Commander Pauline Shields said: "Once again our community has been disrupted and the lives of residents put at risk by an element intent on causing loss of life and disruption.
Although investigations are at an early stage it is our assessment at present, that this vehicle was destined for Lisnaskea PSNI station.
District Commander Pauline Shields
"The people responsible for this have no regard for the lives of anyone in our community. It is fortunate that no-one was killed or seriously injured as a result of this reckless act.
"The people who carried out this act are not part of the society within which the majority of people of Northern Ireland wish to live. The subsequent complex operation has tied up resources that would otherwise be dealing with community issues. We would thank members of the public for their co-operation and patience during this clearance operation."
The security alert in the area has now ended.
The vehicle and the bomb have been taken away for further forensic examination.
UTV's North West Correspondent Mark McFadden, who was at the scene, said: "The scene has now been cleared by police and the road is reopened.
"Army bomb experts worked through the night to defuse this device, which is believed to have been destined for Lisnaskea Police Station about 10 miles away.
"It is a worrying development."
Meanwhile the finger of blame is already being pointed at dissident republicans.
Police want to hear from anyone who travelled along the Derrylin Road - which is part of the main arterial link between Dublin and Enniskillen - between Thursday night and the early hours of Friday and who may have witnessed any suspicious persons or vehicles.
The car at the centre of the alert was found around 16 miles from the Lough Erne resort, which will host the G8 conference in June.
Eight of the world's most powerful leaders, including US president Barack Obama and Russian premier Vladimir Putin, are expected to attend this summer.
The discovery comes after a string of foiled attacks on police in recent weeks, including a mortar bomb found near New Barnsley station in Belfast, an explosion close to three officers along a coastal pathway in Newtownabbey, and a van which was intercepted in Londonderry on its way to a PSNI station, carrying four primed mortar bombs.
Lisnaskea police station is in a built up area with homes and churches nearby. Had this bomb been detonated in that locality there would have been carnage.
Arlene Foster
Local UUP representative Tom Elliott condemned those responsible for the alert.
"The community of Northern Ireland doesn't want this type of activity, they don't want bombs and they don't want people being murdered and their lives disrupted," he told UTV.
"The people who were evacuated from their homes included a 91-year-old lady for possibly two nights, it's disgraceful."
Fermanagh and South Tyrone DUP MLA Arlene Foster said the bomb would have caused "carnage".
She added: "Those behind this bomb were clearly intent on taking life and causing mass destruction. It would seem that these evil terrorists had to abandon the transport of this bomb. The police are to be congratulated on the level of security around the County.
"When we look at the number of failed terrorist attempts across the province, it is clear that the police is successful both at gathering intelligence and also at putting that knowledge to use. It is important that our security services now bring people before our courts and ultimately secure prosecutions."
Meanwhile, Fermanagh and South Tyrone MLA Phil Flanagan said the actions of the "faceless" people behind the attack are futile.
The Sinn Féin representative added: "They do not enjoy any support in this community and in fact no one knows what they are trying to achieve because they have yet to explain how their actions would deliver Irish unity.
"They should desist from such activities that recklessly and needlessly put lives in danger and join with the rest of us in trying to build a better Ireland for all of our people."
Northern Ireland Secretary Theresa Villiers said: "The abandoned device dealt with by PSNI sadly reminds us that there are still a small minority who are determined to damage communities and cause death and disruption.
"Those responsible for it have neither mandate nor legitimacy; they are totally out of touch with what the vast majority of people in Northern Ireland want.
"Acts like this only serve to strengthen our resolve against those terrorists who have nothing to offer Northern Ireland except mayhem and destruction."
Policing Board Chair Brian Rea said: "Thankfully this device did not reach its intended destination. Yet again lives in the community have been put at risk by a minority whose actions are unwanted by the majority.
"In dealing with the device the police and army bomb disposal experts had to work in very difficult conditions and we are very grateful for the work they do on our behalf."