The opening batsman passed the milestone as the home team reached lunch at 59 for one. Australia trailed India by 27 runs and the match was headed for an almost certain draw with only two sessions left.
Hayden was unbeaten on 42 with Ricky Ponting on 15. The only man out was first innings centurion Justin Langer, who went for a duck when he edged Ajit Agarkar to wicketkeeper Parthiv Patel with the total on six.
India led by 86 on first innings after being bowled out for 409.
Thirty-nine runs ahead overnight, India lost their last four wickets for 47 to end any remote chance of forcing a result after the first three days were interrupted by rain.
Fast bowler Andy Bichel triggered the collapse on the fifth morning when he had Agarkar caught by Hayden for 12
Bichel then held a spectacular outfield catch in the next over by Jason Gillespie to get rid of Patel without addition to his overnight 37.
Harbhajan Singh and Zaheer Khan added a quick 41 for the ninth wicket before Stuart MacGill mopped up the tail.
The leg spinner bowled Khan for 27 and trapped Ashish Nehra leg before wicket for a duck to leave Harbhajan stranded on 19 not out.
MacGill and Gillespie finished with four wickets each. Indian captain Saurav Ganguly top scored with 144 while Vangipurappu Laxman made 75.