Seven-time grand slam winner Williams and 2008 French Open champion Ivanovic came to Auckland as the event's drawcards.
Williams, who as the world No.47 is unseeded, made it through to the title decider via a walk-over after American compatriot Jamie Hampton withdrew with a hip injury.
Ivanovic was impressive in dispatching Flipkens 6-0 7-6 (7-3) in 70 minutes in a clash between the respective No.2 and No.3 seeds.
Ivanovic raced through the first set, the Serbian setting up many of her points with her solid serves, which she backed up with accurate shot-making.
"It's something you work towards," she said of her performance in the opening set.
"It really was almost without mistake. I served well, I hit the ball good, I had good timing and I was aggressive too."
Flipkens improved her own serve in the second set, avoiding breaks, but she couldn't manufacture one break-point opportunity herself.
A rare Ivanovic double-fault had her behind early in the tie-break.
But the world No.16 then took control with four points in a row and went on to close out the contest with her first match point.
Williams and Ivanovic have met nine times before, with Williams winning eight.
Ivanovic's victory was in the quarter-finals of the 2008 Australian Open on the way to finishing runner-up to Russian Maria Sharapova.
She admitted she had struggled against both Venus and sister Serena's big serves.
"Sometimes that's overwhelming, when you can see that coming at you," she said.
"But over the years, you get used to it a little bit and you mature and become more calm and you handle the situation differently."
Hampton, the fifth seed, picked up her hip injury in a morning practice session.
"I was taking a couple of extra swings and I just jammed my hip," she said.
"I spoke with the physio and doctor and there's a possibility I can make it worse if I played."
Hampton was confident of being right for the Australian Open, saying she "probably" would have played against Williams if the year's first grand slam wasn't so close.