Gaddafi was killed today following an assault on his hometown of Sirte. He ruled Libya for 42 years before being overthrown by rebels at the end of August.
National Transitional Council (NTC) Prime Minister Mahmoud Jibril confirmed the death in a news conference.
The Secretary General of the World Evangelical Alliance (WEA), Dr Geoff Tunnicliffe, said the day would be remembered with "sadness" by those close to the leader while others would be thinking about those who "deeply suffered under his oppressive regime".
Dr Tunnicliffe called for an end to all hostilities in the country so that the process of reconstruction can begin.
"Our prayer is that this new chapter will improve the welfare for all of Libya’s people as well as create new freedoms of religion in the country," he said.
"On this kind of foundation families, communities and the nation of Libya can flourish. It is also our prayer that other conflicts in the region will be resolved in a more peaceful manner and all people will be given the opportunity to find genuine freedom."
Associate Secretary General of the WEA, Gordon Showell-Rogers, called for prayer as the country embraces a new future.
"The WEA asks Christians to pray for the people and the interim government of Libya in the light of Colonel Muammar Gaddafi’s death - which will inevitably usher in a new era in the country," he said.
"Our prayer is that this new chapter will be better for all Libya’s people, and that, among other things, there may be new freedoms of religion in the country."
Dr Harry Hagopian, senior Middle East adviser to the Roman Catholic Church in England and Wales, said it was a "remarkable day" for Libya after 42 years of despotic rule under Gaddafi.
The leader's death, he said, had effectively answered concerns that he and his supporters would continue to cause trouble for the country despite his overthrow.
Dr Hagopian called for caution, however, as he echoed the sentiments of UN Secretary General Ban Ki-moon, who said that Gaddafi's death is only the "end of the beginning".
"It is a huge boost for the NTC but let's not get too excited because there is a huge road ahead and the death and killing of Gaddafi should not be looked at with too much glee," said Dr Hagopian.
"People should be able to look forward and that means coming together to start the political reconstruction."
In addition to the process of building democracy, Mr Hagopian said there was need for a "process of healing" after months of conflict and the reality of entrenched tribal divisions.
"As much as Gaddafi and his circle were reviled, there are still many people in Libya who are either related to him by blood in the tribe or by marriage.
"Therefore, in a small country with hardly more than six million people, it is important to make sure that not more polarisation takes place but rather that a process of healing takes place.
"That process of healing is very, very important if we are to see Libya come out of the mentality of the 60s and 70s, and into the 21st century," he said.
News of Gaddafi's death was welcomed by Prime Minister David Cameron, who said it was a day to remember Gaddafi’s victims.
"I think today is a day to remember all of Colonel Gaddafi's victims, from those who died in connection with the Pan Am flight over Lockerbie, to Yvonne Fletcher in a London street, and obviously all the victims of IRA terrorism who died through their use of Libyan Semtex," he said.
Mr Cameron said the UK would help Libya as it goes forward.
"People in Libya today have an even greater chance after this news of building themselves a strong and democratic future.
“I am proud of the role that Britain has played in helping them to bring that about and I pay tribute to the bravery of the Libyans who helped to liberate their country.
“We will help them, we will work with them and that is what I want to say today."
Gaddafi’s death follows weeks of fierce fighting to take hold of Sirte, one of the ex-leader’s last strongholds.
Arabic TV channels showed video footage of fighters crowding around two drainage pipes. Gaddafi was reportedly trying to hide in one before being dragged out and shot dead by a fighter. Images show Gaddafi appearing lifeless and covered in blood.
Media reports show scenes of jubilation in the centre of Sirte and among NTC forces, as well as in the capital, Tripoli.