Ed Cowan (46) and Michael Clarke (26) also spent useful time at the crease in perfect batting conditions to help their side reach a target of 260 by mid-afternoon.
Khawaja top-scored with 73, while Hughes added 50 to his first innings 76 not out and Haddin made a brisk 52 not out. Spinner George Dockrell delayed the inevitable with three for 78, but the outcome was never in doubt after the Australians began the day on 36 without loss.
Mumbai Roundup: 9 incidents that took place this week
Photos: Ajay Devgn, Parineeti, Tabu at 'Golmaal Again' trailer launch
Photos: Dipika Pallikal Karthik oozes oomph in bikinis and sarees
Photos: Kareena Kapoor Khan's grand birthday bash
Photos: 'Dangal' girls Sanya Malhotra, Fatima Sana Shaikh's dinner outing