Khawaja brought up his ninth test century just before the tea interval, completing his redemption story.
Khawaja's masterclass ended on 137, with Broad claiming a well-deserved five-wicket haul – his second on Australian soil. Skipper Pat Cummins declared the Australian innings to a close on 416-8.
Australia's day came to a disappointing end, however, with Mitchell Starc taking a wicket on a no-ball in the penultimate over.
Starc found the outside edge of England opener Zak Crawley, with David Warner taking the catch at first slip.
As the Australians celebrated the breakthrough, replays showed that Starc had overstepped the popping crease.
Crawley was gifted an extra life on 0, and England's openers survived to stumps.
England will resume at 13 without loss on day three, still trailing Australia by 403 runs.