Doug Bracewell dismissed David Warner and Trent Boult removed opening batsman Joe Burns and captain Steven Smith to leave Australia wobbling at 66-3, still perilously short of their 187-run victory target.
But Voges and Marsh survived the stiffest of examinations as the pink ball, developed specially for the first day-night test, hooped around on a sunny afternoon at Adelaide Oval.
Voges survived a review for lbw in the final over before the break to be 27 not out, with Marsh unbeaten on 24, the pair having built a 47-run partnership to push Australia to 113-3.
Further challenges will come for the duo, who must negotiate the evening session, when the swinging ball can be difficult for the batsmen to see clearly under the floodlights.
Warner and Burns got Australia’s chase off to a flying start, poaching a run a ball to reach 30 after five overs before Burns was trapped lbw for 11 by Boult, having not played a shot.
In the 11th over, the pressure told on Australia captain Smith, who top-edged a shot high on the leg-side but was dropped on two runs by a back-pedalling Mitchell Santner in the full glare of the sun.
Doug Bracewell limited the damage, however, dismissing Warner for 35, the opener wafting at a shorter delivery and sending a nick flying to Tim Southee in the slips.
Seven balls later left-armer Boult struck a decisive blow, dismissing Smith lbw for 14 to leave Australia wobbling at 66-3.
But Voges and Marsh survived a tense hour to guide Australia’s innings past 100 runs.
Josh Hazlewood earlier finished with career-best figures of 6-70 as New Zealand, who resumed the day on 116-5, were bowled out for 208, adding 92 runs from their last five wickets.
Hazlewood struck with the ninth ball of the day to remove BJ Watling for seven, the wicketkeeper edging to Smith in the slips, and the paceman had his fifth victim of the innings when Mark Craig nicked behind for 15.
Bracewell and spin-bowling all-rounder Santner built a useful 35-run partnership but Lyon ended it by luring Santner down the pitch and having him stumped for 45.
Pace bowling all-rounder Mitchell Marsh captured his third wicket of the innings when Tim Southee, on 16, miscued a pull with Lyon jogging along the rope to take the catch.
Bracewell finished unbeaten on 27, with Hazlewood wrapping up the innings by bowling Boult for five.