Rights groups were angered by the presence of countries such as Niger, where a military government took power in a coup five months ago and where French nuclear firm Areva has lucrative uranium mining contracts.
But Sarkozy insisted the parade was not about colonial "nostalgia" during an address to the African leaders on Tuesday.
"I know very well the notion of privileged and special relations, this flood of suspicions and fantasies, but the time has come to face up to it together, without inhibitions and without looking back," he said.
Herve Morin, the defence minister, also dismissed the criticism, saying there was "no indication" that there were war criminals among Sarkozy's guests.
About 12 African heads of state attended the parade along with Sarkozy and his wife, Carla Bruni.
The parade saw fighter jets fly over the city, followed by African troops marching down the Champs Elysees avenue, headed by an all-female unit from Benin.
They were followed by French troops, firemen, police, armoured vehicles and marching bands.
The heads of state from Benin, Burkina Faso, Cameroon, Central African Republic, Congo, Gabon, Mali, Mauritania, Niger, Senegal, Chad and Togo sat watching from the official stand.
Ivory Coast was represented by a government minister but did not take part in the march. Forces from Madagascar also joined the parade.
Bastille day is an annual French holiday that marks the storming of the Bastille prison on July 14, 1789, signalling the start of the French Revolution.