The rebels are seeking to topple Idriss Deby, Chad's president.
An initial French draft had called on UN members to support Deby "by all necessary means", but the final wording was changed to satisfy Russian objections to what was seen as a reference to military aid.
Speaking before the Security Council issued its statement, Nicolas Sarkozy, the French president, said France and the EU would send troops only with the council's approval.
"We must avoid a conflict in Chad by supporting the legitimate government," Sarkozy said during a visit to Bucharest.
"In no region should weapons be a way to come to power."
But Bernard Kouchner, the French foreign minister, said Ndjamena was under government control for now and he did not foresee French troops entering combat.
"We do not have the intention of putting French troops on alert more than they already are and of launching military operations," he said in Paris.
There were reports of renewed shelling on Monday in Chad, as rebels returned to the city.
Inside Ndjamena the scene was "bloody and chaotic", one aid worker was quoted by the Associated Press as saying.
Aid agencies also said that hundreds of civilians had been injured by stray bullets.
There has been no indication of the toll from the two days of fighting but Medecins sans Frontieres, the international medical organisation, said it had operated on about 50 people in the capital.
The French military, which has been flying foreigners from Ndjamena to Gabon, said on Monday under 300 foreign nationals were still waiting to be evacuated from the capital.
The rebels first attacked Ndjamena on Friday.
A force of 1,000-1,500 fighters, equipped with pickup trucks mounted with machine guns, arrived on the capital's outskirts after a three-day push across the desert from Chad's eastern border with Sudan.
President Idriss Deby seized power in a Libyan-backed coup in 1990
He went on to win the Chad's first two
multi-party elections in 1996 and 2001
A ceasefire signed between Deby and four rebel groups in October recently collapsed
The largest rebel group, the Union of Forces for Democracy and Development, is led by a former minister who accuses Deby of corruption
Click here for more on Chad's spiral into conflict
They penetrated the city early on Saturday, reportedly trapping Deby in his palace.
The government launched a counterattack on Sunday and the rebels pulled back that evening in what they said was a tactical withdrawal to give Ndjamena's inhabitants a chance to flee.
Analysts fear the fighting could broaden into a wider regional conflict.
Monday's UN statement also urged "all states in the region ... [to respect] their common border".
Some Chadian officials have charged that Sudan supported rebel attacks on a town close to Sudan's Darfur region, though Khartoum has denied any involvement.
The US said on Monday that it had warned the Sudanese government to stop any support it might be giving the rebels.
"We've gone directly to very high levels of the Sudanese government to say that if there is any support ... to these rebels, that should end immediately," Sean McCormack, the US state department spokesman, said.
For years Chad and Sudan have accused each other of supporting rebel groups in each others territory.