Ms Kawaguchi argued the Japanese case
The deal was voted on by a plenary session of the Kyoto signatories on Saturday.
"There is agreement on everything by everyone," said French environment minister Yves Cochet.
The Kyoto Protocol calls on nearly 40 industrial countries to limit or reduce their emissions of greenhouse gases - primarily carbon dioxide from industry and cars - which some scientists believe are rapidly raising global temperatures.
The accord assigns each country a target and sets an average 5.2% emission reduction from 1990 levels, to be achieved by 2012 - although environmental groups say the reality is nearer 2%.
Key umbrella
One of the main sticking points has been the issue of carbon "sinks" - forests, grassland and other vegetation which absorb carbon dioxide, and can be counted against a country's emissions reduction target.
With the US - the world's biggest emitter of greenhouse gasses - definitely refusing to ratify the protocol, the support of Australia, Canada, Japan and Russia became vital.
This tactical alliance is called the Umbrella Group, and it had been blocking agreements on certain key points.
Substantial concessions had already been made to Russia in the last round of talks in Bonn in July.
Russia was allowed to argue that its vast forests soaked up at least 17 million metric tonnes of carbon a year, thus sparing it the need to reduce its use of coal and oil by that amount.
The exact details of the final deal are not yet clear, but it seems apparent that Russia will be able to sell its excess energy credits and that Japan will be able to buy them.
The EU says it will ratify Kyoto by 2002, but its support alone will not be enough to bring the treaty into force.
For that to happen, Kyoto must be ratified by at least 55 countries responsible for 55% of 1990's emissions.
The BBC correspondent at the talks, Elizabeth Blunt, says that one notable feature has been the improved relations between the United States and the other participants.
The United States, she says, now recognises climate change as a real problem requiring action.
Now that the "rule book" for Kyoto has been drawn up, the US can see what participation would involve.
The Dutch Environment Minister Jan Pronk said in Marrakech on Saturday that he believed the United States would eventually rejoin the process.