Due to the popularity of what was meant to be just a summer only service, the UK regional airline has said it will continue to operate flights until 28 October, 2011.
And Eastern Airways has said that the route will return in April 2012.
Flights operate on Monday, Friday and Sunday using a 29-seater Jetstream 41 aircraft, with fares starting from £75 one way, including taxes.
Kay Ryan, Eastern Airways’ commercial director, said: "We introduced the new seasonal service from Southampton as part of our wider development plans in Dijon providing an international link to the south of England.
"Flights have proved popular over the summer season and we’ve taken a decision to extend the service with it now running until the end of October. These services will then be reintroduced in April 2012."
Monday flights depart Southampton at 12.50pm, arriving in Dijon at 3.40pm local time. Services leave Dijon at 11.30am and arrive in Southampton at 12.20pm local time.
Flights on Fridays take off from Southampton at 1.50pm, landing in Dijon at 4.40pm local time. Services leave Dijon at 12.30pm and arrive in Southampton at 1.20pm local time.
Sunday services leave Southampton at 1.40pm, arriving at 4.30pm local time. Flights leave Dijon at 12.10pm and land in Southampton at 1.10pm local time.
Eastern Airways has established a base at Dijon and currently offers domestic flights to Bordeaux, Toulouse and Nantes.