Replying to Australia's massive first-innings score of 551 for four declared, the Sri Lankans were forced to follow on after being dismissed for 211 runs in their first innings. They are now still 122 runs behind their hosts.
Resuming at 80 for two, Vandort - who began the fourth day on 15 - played a patient innings to reach his 50 after lunch as he shared a century partnership with Mahela Jayawardene.
The third-wicket pair batted sensibly to add 102 runs before Jayawardene's departure.
The skipper was on the verge of a half-century himself when he was dismissed for 49, caught behind by Adam Gilchrist off the bowling of debutant Mitchell Johnson.
Vandort's resistance ended when he was bowled between bat and pad to become Stuart MacGill's 200th Test victim.
Thilan Samaraweera was the only other wicket to fall on a day which saw bad light and rain interruptions frustrate the Aussies. Samaraweera contributed 20 before finding Michael Hussey at gully off the bowling of Johnson.
Chamara Silva was unbeaten on five and Prasanna Jayawardene yet to score when bad light brought an end to the day's play.
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