The home side need 169 more runs with ten wickets remaining to clinch a Test match in Hobart dominated by the bowlers.
Australia close in on Trans-Tasman Test series win
Warner was unbeaten on 47 with Hughes on 20 as Australia eyed victory in the second Test as rain brought a premature end to the day's play. Australia are already 1-0 up in the two-match series.
New Zealand collapsed prior to lunch to be dismissed for 226, an overall lead of 240, and despite a delayed start to the second session due to rain, the home side moved into the box seat with one session still to play on day three.
Hughes was under particular scrutiny following his recent run of poor form and batted cautiously during the opening overs as Chris Martin and Trent Boult probed away outside his off stump.
The diminutive left-hander may have received a slice of luck early on when New Zealand captain Ross Taylor opted not to review a not-out decision from umpire Asad Rauf when it appeared Hughes may have gloved the ball onto his hip and through to wicketkeeper Reece Young.
The Black Caps paid closer attention to the state of the ball, however, having it changed twice during the first 10 overs of the Australian innings.
While the bowlers managed to extract some swing early, the regular sideways movement that had been so evident during the first two days was not forthcoming, allowing the Australian openers to settle into their work during the shortened session.
Both players peppered the cover boundary and took full toll of any width from the New Zealand attack in a sign their confidence was returning.
Warner was particularly damaging, scoring more freely than Hughes, and was very impressive on the drive, both straight past the bowler and through the off-side.
Earlier, disciplined bowling and sharp catching saw Australia claw their way back into the match by removing the New Zealand tail cheaply.
James Pattinson continued his impressive start in Test cricket, removing the dangerous Ross Taylor for 56 and undoing Dean Brownlie (21) with a sharp, short delivery that tailed in towards the right hander and was snapped up by Haddin after ballooning off the former West Australian's thumb.
Peter Siddle also continued his impressive return to form and was rewarded for consistent line and length with the wickets of Kane Williamson and Reece Young.
The Young dismissal reduced the tourists to 190 for seven in the shadows of lunch and exposed a lower order that has proved brittle so far this series.
After some lusty blows, Tim Southee was the fifth Black Cap wicket to fall, caught in the deep by Mike Hussey off Nathan Lyon's bowling and Doug Bracewell followed two balls later, bowled by the South Australian off-spinner.
Lyon took his third wicket when he had Boult caught in the deep to close the New Zealand innings.
Brownlie, the form batsman for New Zealand so far this series, had been softened up by left-arm quick Mitchell Starc in the overs leading up to his dismissal, wearing a painful blow above the wrist from a similar delivery to that which eventually dismissed him.
His partnership with Taylor frustrated Australia for the best part of an hour, the gritty pair looking to set a platform from which to push their lead well beyond 200 as the day unfolded, but it was not to be as Pattinson bobbed up to strike twice from the southern end of Blundstone Arena.
New Zealand started the day well-positioned at 139 for three, a lead of 153 over the Australians, but their morning did not start well when Williamson, 34 not out overnight, was sent packing in the first over of the day.
Siddle managed to find the outside edge of the youngster's blade and the ball was pouched expertly by Ricky Ponting, low and to his right-hand-side at second slip.
Clarke matched Ponting's safe mitts with clean hands of his own when Pattinson found Taylor's edge and this must have come as a relief to both bowler and captain after the young Victorian quick had dropped a return catch when Taylor was on 48.