The wholly owned subsidiary of Air India would fly between the two cities on Mondays, Wednesdays and Saturdays.
Alliance Air connects 53 destinations within India with 113 destinations per day. Jaffna is the 54th destination for the airline.
Commemorating the launch of the service, Governor of the Northern Provincial Council of Sri Lanka Suren Raghavan took part in the journey.
The Council website quoted Raghavan as saying he expects the new airport in Jaffna would create new relationships as well as trade links between the two countries.
The Chennai-Jaffna flight service has resumed after a gap of 41 years. The flight operations were suspended during the decades old civil war in Sri Lanka.
Jaffna International Airport was earlier known as Palaly airport, which was used as a military air base and for domestic flights.
Sri Lankan President Sirisena and Prime Minister Ranil Wickremesinghe had formally unveiled a plaque commemorating the inauguration of the airport on October 17.
In a statement issued on Monday, Alliance Air said the flight service was special in many ways.
“Apart from being Alliance Air’s maiden international foray, it connects Chennai and Jaffna after a gap of 41 years”, the press release said.
Flyers coming to Chennai from New Delhi, Coimbatore, Ahmedabad, Mumbai, Dubai, Thiruvananthapuram and Muscat have the option of connecting onwards to Jaffna over Chennai.
“A proud moment-second airline in Air India group goes global”, Air India Chairman and Managing Director Ashwani Lohani said.
Ahead of the launch, Alliance Air CEO, C S Subbiah said “it brings us immense pleasure after spearheading efforts connecting unique regional routes within India under UDAN, we are now set to fly international”.
“This will be the first non-stop service between Chennai and Jaffna” he said.
Fares on the Chennai-Jaffna route are priced at Rs 3,990 while on return journey it is at Rs 3,190 plus government taxes.