French readers queued at dawn for copies to support the satirical newspaper, even as al Qaeda's branch in Yemen claimed responsibility for the attack last week, saying it ordered the killings because it deemed the weekly had insulted the Prophet.
Across the Middle East, Muslim leaders who have denounced the attack in which 12 people died called for calm, while criticising Charlie Hebdo's decision to publish a fresh caricature of Mohammad.
President Francois Hollande visited France's Charles de Gaulle aircraft carrier in the Mediterranean and said it was ready to support military operations against Islamic State in Iraq "in close cooperation with coalition forces".
Also on Wednesday, the Interior Ministry said over 50 cases of people voicing support for terrorism had been registered since the attack on Charlie Hebdo's Paris office and the subsequent killings of a policewoman and four people at a Jewish supermarket.
Millions of copies of the "survivors' edition" were printed, dwarfing the usual 60,000 print run. On its cover, a tearful Mohammad holds a "Je suis Charlie" sign under the words "All is forgiven."
Inside, one cartoon showed jihadists saying: "We shouldn't touch Charlie people ... otherwise they will look like martyrs and, once in heaven, these bastards will steal our virgins."
This week's edition underlined the irony of how the victims had been commemorated at Notre-Dame cathedral in Paris.
"What makes us laugh most is that the bells of Notre-Dame rang in our honour," read an editorial in the newspaper, which emerged from the 1968 counter-culture movement and has long mocked all religions and pillars of the establishment.
David Sullo, standing at the end of a queue of two dozen people at a central Paris kiosk, said he'd never bought it before: "It's not quite my political stripes, but it's important for me to buy it today and support freedom of expression."
Prime Minister Manuel Valls, himself a frequent target of the weekly's caricatures, left a cabinet meeting with a copy tucked under his arm.
"BATTLE OF PARIS"
In a video posted on YouTube, Al Qaeda's Yemen branch said its leadership had ordered last Wednesday's attack on Charlie Hebdo.
"As for the blessed Battle of Paris, we, the Organisation of al Qaeda al Jihad in the Arabian Peninsula, claim responsibility for this operation as vengeance for the Messenger of God," said Nasser bin Ali al-Ansi, the group's main ideologue in Yemen.
Ansi said the strike was the "implementation" of an order by al Qaeda leader Ayman al-Zawahri. It was not immediately possible to verify the authenticity of the recording.
The two brothers who attacked Charlie Hebdo and a third gunman who killed the policewoman and hostages at the kosher supermarket all died in police raids.
Defenders praised the cover for upholding the newspaper's satirical mission, proclaiming its right to free speech while maintaining a mournful tone and a peaceful message.
Jonathan Jones, art critic for Britain's Guardian newspaper, called the cover "a life-affirming work of art".
"Funny people were killed for being funny. This new cover is the only possible response - a response that makes you laugh," he wrote. Belgium's Le Soir wrote: "Not publishing the edition would have been like a second death for the victims."
Several German newspapers reprinted the new cover. It filled the back page of the top-selling Bild daily, whose columnist Franz Josef Wagner praised it highly. "It is sarcasm, it is biting ridicule ... they are mocking the murderers," he wrote.
In the Middle East, it was branded a new provocation that could create a backlash. Publishing the cartoons "shows contempt" for Muslim feelings, said the Grand Mufti of Jerusalem and Palestinian lands, Mohammed Hussein.
Iran's foreign minister Mohammad Jawad Zarif said serious dialogue with the West would be easier if it respected Muslim sensitivities. "We believe that sanctities need to be respected," he said before nuclear talks in Geneva with U.S. Secretary of State John Kerry. "We won't be able to engage in a serious dialogue if we start disrespecting each other's values."
A court in the southeastern Turkish city of Diyarbakir ruled in favour of blocking four websites that ran the cover.
"Those crass people proud of attacking religions are inflaming Islamophobia. This mentality, whatever vehicle it uses, is a threat to world peace," Deputy Prime Minister Yalcin Akdogan wrote on Twitter.
Algeria's independent Arab language daily Echorouk ran its own front page cartoon showing a man carrying a "Je suis Charlie" placard next to an army tank crushing placards from Palestine, Mali, Gaza, Iraq and Syria. Above, the headline reads: "We are all Mohammad".
Samir Mahmoud, a retired engineer in Cairo, said the cartoons "have no meaning, they should not affect us. We as Muslims are bigger and stronger than some cartoon".
All proceeds from the sale of this week's edition will go directly to Charlie Hebdo, a windfall for a publication that had been struggling financially.
While many French people enthusiastically supported the weekly's decision to put another cartoon of Mohammad on its cover, some expressed concern it would provoke more tension.
Bordeaux mosque rector Tareq Oubrou urged French Muslims not to overreact to the new cartoons. "I don't think the prophet of Islam needs stupid or excited reactions," he told BFM-TV. "Freedom has its downsides and we must live with them."
Dieudonne M'bala M'bala, a French comedian convicted in the past for anti-Semitic comments, was held for questioning on charges of glorifying terrorism for writing on Facebook "Je suis Charlie Coulibaly", adding the surname of one of the gunmen.
France will announce next week a set of anti-terrorism measures, officials said. New resources will be released for surveillance and France could look at widening the policy of isolating radical prisoners.
Hollande, the most unpopular French president in survey history over his failure to kickstart the economy, has come out of the crisis well, with 85 percent of French approving of his handling of it, a poll showed on Wednesday.
