The talks were earlier extended by a day as negotiators from nearly 200 countries haggled through the night to finalize details of a deal that allowed the 1997 pact to live on for another commitment period.
The pact, which controls the greenhouse gas emissions of rich countries, was originally due to expire this year.
However, the new agreement only covers developed nations whose share of world greenhouse gas emissions is less than 15 per cent.
The protocol locks in only developed nations, excluding major developing polluters such as China and India, as well as the US which refuses to ratify it.
The Protocol got extension with the EU, Australia, Switzerland and eight other industrialised nations signing up for binding emission cuts by 2020.
Conference Chairman Abdullah bin Hamad al-Attiyah, who "begged" to the countries to offer something out of the conference, termed the deal as the Doha Climate Gateway.
The deal also includes agreement to scale up funding to help poor countries deal with global warming and convert to planet-friendlier energy sources.
The 12-day meeting in Doha also aimed to adopt in 2015 a wider treaty that would apply to all countries and eventually replace the Kyoto Protocol.
US rejected the idea of equity by refusing to associate itself to any new agreement that is under the Convention. Russia outrightly rejected proposal while G77 and China, BASIC groups support Doha outcome.
Amid Russia's continued protests against his decision, President Al-Attiyah said, "It was my sense that the decision reflects the will of party as a whole to resolve Doha".
The developments came after negotiators worked through the night over intrinsic details and language that could be acceptable to all, with discussions continuing till late in the day and finally clinching the deal.
"It was a long day," said Al-Attiyah, summing up the sentiment of the tired and weary negotiators, some of whom were seen catching small naps in the plenary as they waited for the dissent-hit slow proceedings to move.
"While everyone is unhappy but everyone wants an agreement (nevertheless). I didn't want to open the Pandora's box by opening the entire texts again because we will never finish. I am not carrying a magic trick, but please help me, this is at least a good text, we cannot find a text satisfying everyone.
"I beg you to help the President, this is my final begging to accept what we can offer," he told delegates earlier in the day.
The 12 days of talks saw bitter wrangling over the poor countries' insistence that the rich nations make substantial pledges to cut greenhouse gases and finance mitigation and adaption efforts in the poor countries that have not historically contributed to global warming but are presently the most vulnerable.
"The talks failed to deliver increased cuts to carbon pollution, nor did they provide any credible pathway to USD 100 billion per year in finance by 2020 to help the poorest countries deal with climate change," the 700 NGOs, who are members of Climate Action Network-International, said in a statement while reacting on the deal.
"Two weeks of negotiations have not altered that path and that politicians need to reflect the consensus around climate change through funds, targets and effective action," said Greenpeace International executive director Kumi Naidoo.
While WWF head of delegation, Tasneem Essop, said Doha was supposed to be an important element in setting up for a fair, ambitious and binding deal in 2015 and therefore needed to rebuild trust and instill equity.
"These talks have failed the climate and they have failed developing nations," Essop said.