Warner and Khawaja took the record second wicket stand at the Waca, previously 259 by Wayne Phillips and Graham Yallop in 1983 against Pakistan, to 302.
They'd also comfortably overtaken Michael Slater and David Boon's second wicket record against New Zealand, 235 at Hobart in1993 and Warner had the second highest score by an individual at the Waca, trailing only Matthew Hayden's 380 against Zimbabwe 13 years ago.
New Zealand needed to win the toss on a broiling day and a pitch full of runs. They didn't and were made to suffer.
They had two appeals for lbw rejected inside the first three hours - Burns on 26 off Tim Southee, but replays showed he nicked it into his pads; and Warner on 78 off Trent Boult. Replays showed the ball hitting the top of the stumps, therefore it came back to umpire S. Ravi's original not out call.
Soon after, offspinner Mark Craig had Khawaja caught at the wicket, but when umpire Nigel Llong got it wrong, New Zealand had no referrals left.
Southee, confirmed in the side shortly before the start, after recovering from his damaged back, was the pick of the seamers.
Boult, out of sorts in the first test, continued to struggle, Warner flaying three boundaries in his first over with the second new ball late in the day.
Craig was unable to keep things tight, Henry had the odd good moment and Bracewell was unable to make an impact.