The Boeing 737-8009 flight, DJ64, was scheduled to arrive at 3.25pm to a water-arch welcome, but a minor fault with an air-conditioning fuse, discovered while the plane was still grounded at Brisbane, meant it did not land until about 4.45pm.
Pacific Blue spokesman Phil Boeyen said the company would always err on the side of caution.
Dunedin deputy mayor Syd Brown said the flights would bring business connections to Dunedin.
Three flights a week meant 540 seats a week, which would bring a lot of economic activity to the city.
The flight from Brisbane yesterday, which was almost full, was called a "penguin party in the sky", with passengers given the chance to win tourism packages in Dunedin, as well as a jaffa roll and auction, the proceeds of which would go to the Yellow-eyed Penguin Trust.
Two of about 10 people who came to Dunedin airport dressed as penguins were given return flights to Brisbane.
Tourism Dunedin chief executive Hamish Saxton said six Queensland journalists and seven travel agents came to Dunedin on the flight and were being hosted in the city over the next few days.
Mr Saxton said Dunedin people needed to give Pacific Blue a reason to expand its Dunedin service.
The airline has offered domestic flights from Dunedin for more than a year.
Mr Boeyen said "anything" was possible and the airline would see what demand was like for the Brisbane service.
It was possible a Sydney and Melbourne link could be added.
Dunedin International Airport chief executive John McCall said it was "a great day" for the city as competition in the transtasman service could only be good news for passengers.
Mr McCall said he was constantly in talks with other airlines, including Jetstar, about flying into Dunedin, but the airport could not cater for some of the bigger aeroplanes.
Direct Air New Zealand flights to Sydney and Melbourne would resume in December, although they had been confirmed only through to the end of January, Mr McCall said.
The return flight to Brisbane was full.
