To keep as many planes in the air as possible in the middle of a holiday period, the airline limited short-haul flights to 100 passengers on Saturday and Sunday so that numbers of flight stewards respected safety norms. That meant many aircraft were running with empty seats while people were turned away.
Unions have called flight stewards to strike over five days until and including Wednesday. One of their main grievances is a plan to reduce staffing on long-haul trips.
The carrier scrapped nine long-haul flights to destinations such as Tokyo, New York and Abu Dhabi but predicted only half as many cancellations on long-distance routes for Monday.
In a statement on Sunday evening, it said it had managed to operate more flights than the 80 percent it had initially forecast, saying 87 percent of flights got off the ground on Saturday and 88 percent on Sunday.
Tuesday, November 1 is a public holiday in France and many take Monday off to extend the weekend break. It also falls during the mid-term school holidays.
Disruption at the main Paris airports, Charles de Gaulle and Orly, was limited to an extent by advance warning that 20 percent of around 1,000 daily flights would be scrapped.
The airline has said the protest is incomprehensible and in a statement over the weekend denounced the fact that it had been taken hostage at such a busy time.
Some travellers interviewed by local TV stations said they would return by train while others said that they would wait, hoping they would be able to return by plane in the coming days.
Government minister Nathalie Kosciusko-Morizet criticised the unions, primarily over the timing.
Air France is in a delicate position, she told Europe 1 radio in an interview. She said she hoped to get away herself on an evening flight to Israel for government business.
Shares in Air France-KLM, which is due to publish financial results on November 9, took a hit this week when a media outlet said it was preparing to issue a profit warning. The carrier said last Tuesday, in response to that media report, that it would not publish any financial information before November 9.
Air France-KLM, Europe's largest airline when measured by revenue, was formed by the merger in 2004 of Air France and Dutch carrier KLM. The industrial action concerns only the French side of the operation.
Another major world airline, Australia's Qantas Airways
(Additional reporting by Patrick Vignal; Editing by Jon Hemming)