Ten years after claiming her first title as a 15-year-old in 2001, Jones came home strongly to win the event, clocking one minute 6.18 seconds ahead of Sarah Katsoulis (1:07.24).
It was Jones's only chance to book a spot on the team for July's world championships in Shanghai as she is not contesting the 200m breaststroke event.
"That's what I had to do, just make the team. I actually had a lot of pressure on myself from me because I've only got one event I can make the team in," Jones said.
"I'm not very happy with the time to be honest, that's not going to get me very far.
"If you want medals you're going to have to be swimming pretty quick this year so I've got to go back to the drawing board and see what's going on."
Jones, 25, said her desire was stronger than ever building towards next year's London Olympics after taking a break from swimming in 2009.
"Since I've come back from my break I'm more hungry now," said Jones, who has seven world titles from four championships.
Emily Seebohm defied a recent bout of swine flu to book a spot at the world championships before collapsing from exhaustion.
Seebohm, 18, who had been ill for several weeks leading into the meet, missed out on her fifth straight 100m backstroke title as Belinda Hocking (59.55secs) claimed a surprise victory.
But Seebohm (1:00.08) held on to finish second and also claim a spot on the team before blacking out on her way back to her change room.
Her coach Matt Brown said Seebohm had "knocked herself into the ground" and would be withdrawn from the rest of this week's meet.
Thomas Fraser-Holmes swam a personal best (1:47.19) to take out the men's 200km freestyle from Kenrick Monk (1:47.53), who missed a spot in the world championship team as his time fell outside the qualifying time set for the event by Australian head coach Leigh Nugent.
Melissa Gorman took out the women's 1500m freestyle in 16:06.98 and was joined on the team by second-placed Jessica Ashwood (16:14.47).
Ben Treffers, 19, claimed his first national title in the 100m backstroke in 53.72 from Hayden Stoeckel (53.87).