Veteran quick bowler James Boyland wound back the clock in a virtuoso performance, which had the Centurions rebound after poor recent form.
Joondalup will be looking for an outright victory in a bid to re-enter the top four, having already secured first-innings points.
Boyland produced a vintage display to take 7-46 in his best performance for the season, with the veteran dominating the Roos, who could manage just 139. Aaron Brunner top-scored for Wanneroo with 42.
Joondalup is 4-178 in response, taking a lead of 39 into the second day.
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Josh Inglis was the hero with 80 not out, as he continues to have a fantastic season, while Jaron Morgan managed a run-a-ball 38.
The Roos’ Chris Quelch, Matthew Dzodzos, Bailey Nylander, and Kyle Millar took a wicket each.