More than 400 of the company's pilots called in sick to protest after two of their colleagues were sacked for setting up a trade union.
The airline and pilots' union said they had agreed to hold talks. The sacked pilots will be re-instated.
The company's executive director reportedly said international flights would resume immediately.
Jet Airways Executive Director Saroj Dutta said, "Flight operations of the airline on international routes would resume immediately while the domestic services would normalise by noon on Sunday, Sep 13."
Announcing the settlement at a news conference, the pilots union National Aviators Guild leader, Sam Thomas said, it has been agreed that the four sacked pilots would be reinstated with immediate effect.
According to media reports, the strike cost the airline, owned by Naresh Goyal, some $8m (£4.79m) a day.