The addition of the new Dunedin to Brisbane service will increase the airline's flights from three to four a week.
Virgin Blue chief executive Mark Pitt said Queensland was one of the low-cost carrier's best-performing destinations, and the Dunedin market had shown "good support" for direct services to Brisbane.
The city was a hub for the airline's international services, and allowed Dunedin travellers to access its "extensive domestic market", he said.
Dunedin International Airport chief executive John McCall said the confirmation of the Friday flight was "good news" and would result in more people travelling across the Tasman for weekends.
He said the extra flight had been discussed as early as six months ago, and was unlikely to be affected by code-share discussions between Air New Zealand and Pacific Blue.
Air New Zealand now flew Dunedin-Brisbane once a week, and that would increase to two flights at the end of June, he said.
Australians made up almost half of all inbound passengers and there was an opportunity to grow that market, and to encourage Otago and Southland residents flying across the Tasman to use the Dunedin-Brisbane services.
A Pacific Blue spokesman said the Friday flights were likely to begin in October, but could be brought forward.
Hamilton also gains one extra weekly Pacific Blue flight to Brisbane - from three to four - but would lose its Hamilton-Sydney service.
