Whincup played down the significance of 100 wins, and said the result today was due to a lack of pace at the end of the race. "I was going for the win, that's what it was all about," he said.
The result meant Van Gisbergen closed the gap on Whincup at the top of the points table to 41 points, with Ford's Mark Winterbottom, who finished fourth yesterday, third.
New Zealand's Scott McLaughlin is still fifth in the standings but finished down the field in 15th. Fabian Coulthard was 10th, Pither 11th, Andre Heimgartner 20th and Craig Baird, who drafted in to replace Aaren Russell for Erebus Motorsport this weekend, 25th.
The race was reduced by a lap when Ford's Cameron Waters broke a tailshaft on the formation lap and had to limp into the garage.
Another Ford driver, DJR/Team Penske's Scott Pye finished the day in 21st after his team put in a mammoth effort to completely rebuild the front end of his Falcon following a high-speed crash earlier in practice.
The Ipswich SuperSprint wraps up tomorrow with a 200km race.