Contact with Fabian Coulthard in the opening laps of Saturday's first qualifying session saw the VIP Petfoods/Lucas Oil Commodore sidelined, putting Van Gisbergen at the rear of both 100km races.
The #97 Commodore bounced back in Sunday qualifying, Van Gisbergen taking fifth, before going on to hold the position over the 45-lap feature.
"We were much happier on Sunday after the weekend that was. The car was much better and we were competitive," Van Gisbergen said.
"Our performance shows how resilient we are. We effectively lost two days of set up, so it was pretty tough but we weren't that far off."
The Kiwi charged to make up lost ground in Saturday's twin sprints, but lamented the clash with Coulthard.
"That's the problem with short qualifying sessions - everyone's got different plans," Van Gisbergen said.
"We were on warm up tyres while they were about to start a run. I had my headlights on letting them know I was going to go through and carry on with my own thing but he moved to the right. I thought he saw me but he didn't, and we hit.
"It was hard racing from that far back. I wasn't comfortable in the car but I pushed hard in both races. We still had some issues from the qualifying crash."
Van Gisbergen is keen finish the year on a high at the Sydney NRMA 500, historically a strong event for the team.
Last year saw the Kiwi on the podium alongside teammate Jonathon Webb on Saturday, before going on to win Sunday's race from pole position.
"It's a crazy place there so we've just got to see what happens. You need to put two strong days together, and it's a new format this year," Van Gisbergen said.
"I've been quick at Homebush since we started going to it, so I'm excited to get back there and give it another go."
The Sydney NRMA 500 is held from 5-7 December.