Five unions representing 76.4 percent of the personnel accepted management's offer of a four-percent pay rise to be spread over 2018 and 2019, the two sides announced.
The main pilots' union, which is holding out for a separate deal, did not sign the accord but Air France said that it was nonetheless "considered valid and will be implemented."
The deal is a feather in the cap of new Air France-KLM CEO Ben Smith, who took the helm in August after a turbulent few months marked by 15 days of strikes, which caused widespread travel disruptions.
Smith, who is Canadian, thanked the various parties "for the quality of our discussions over the past few weeks".
"This way of working between all parties provides Air France and the Air France-KLM Group with a new perspective going forward, and it is my hope that it will ensure the future success of our airlines," he said in a statement.
Air France said the strikes set it back 335 million euros ($385 million).
Smith, the airline's first non-French boss, succeeded Jean-Marc Janaillac who resigned in May after failing to get unions to call off months of strikes.
Under the final deal, workers will receive a two-percent increase for 2018, retroactive to the start of the year, and a further two-percent increase in January 2019.
They had been demanding a 5.1 percent pay hike for the 2012-2017 period.
Farid Slimai, a spokesman for the Unsa-Sol union which represents ground personnel, said the unions finally accepted management's offer as an "act of confidence aimed at Ben Smith" and to help the airline "move on and look to the future.".
Throughout the spring the employees dug in on their demands, saying workers needed to be rewarded for accepting years of salary freezes while Air France-KLM attempted to climb out of the red.
Management argued that their demands would set back Air France-KLM's restructuring efforts and thwart its ability to compete with low-cost carriers like Ryanair and Easyjet.
In the second quarter of 2018, the group posted net profits of 109 million euros, down sharply from 593 million for the same period last year, although that figure was boosted by new accounting rules.
After a four-month hiatus following Janaillac's departure Smith kickstarted new talks in September which culminated in two days of formal negotiations this week.
Slimani said that the unions were finally won over by better terms for low-paid staff, including an increase in the bonus paid to uniformed staff towards the cost of cleaning their garments.
But Smith, who is on a mission to build up the airline's low-cost brands Transavia and Hop, has yet to get pilots on board with his cost-cutting drive.