Workers were protesting against mass job cuts when two managers` shirts were ripped and one was forced to flee over a fence. Several others were injured.
The protest came amid anger over budget cuts across the French economy.
Hundreds of workers were protesting against plans to cut 2,900 jobs, increase pilots` working hours and reduce the size of the fleet, all designed to cut costs by €1.8bn ($2bn; £1.3bn) over two years.
Two managers in particular were targeted - human resources manager Xavier Broseta and senior official Pierre Plissonnier.
They were taking part in a works council meeting about the proposed cuts when hundreds of workers stormed into the Air France headquarters.
""Seven people were injured in the scuffles, including a security guard who was knocked unconscious.
The five workers, along with another colleague, are due to appear in court on 2 December to face criminal charges in connection with the violence.
Air France said a further 11 staff had been suspended for two weeks without pay for breaking into the company`s headquarters, Reuters news agency reported.
Following the protests Air France slashed the number of jobs it planned to cut to fewer than a thousand.
The next Air France works council meeting is on 19 November. Unions have called for industrial action on that date in protest against the disciplinary measures.
At the end of October parent firm Air France-KLM reported a net loss of €158m for the first nine months of this year, compared with a loss of €533m for the corresponding period last year.
"This improvement is however not sufficient to bridge the competitiveness gap with our competitors or to generate the financial resources required to finance the group`s growth," said chairman Alexandre de Juniac, inviting union representatives to resume negotiations.
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