The 31-year-old Jackson was appearing at her fourth Olympic Games after leading the women's basketball team to silver in Beijing four years ago.
Chef de Mission Nick Green said Jackson had been chosen for her leadership qualities on and off the court, but her appointment to carry the flag also followed a row over gender equality in Australia in recent weeks.
Five time Olympic beach volleyballer Natalia Cook said last week, apparently in jest, that she would stage a sit-down protest if she had to walk behind another male flag bearer, while there were also complaints about travel arrangements.
The women's basketball team, who have been runners-up to the United States at the last three Games, flew to London in economy class while the country's men, who have never won a medal, went in business class.
The arrangements were slammed by Australian media and politicians, forcing the country's basketball governing body to say it would review its policy.
The last Australian woman to lead out the team was diver Jenny Donnet in Barcelona in 1992.)