Resuming day two on 361 for two, Australia cruised to 461 for four before declaring their essay after 113 overs.
The highlight of the hosts' innings was Jaques' stellar innings which saw him occupying the crease for a mammoth eight hours during which he faced 331 balls and hit 21 boundaries before India 'A' skipper Y Venugopal Rao trapped him.
Other overnight batsman Travis Birt (130) also completed his well-deserved century and his 210-ball knock included 10 boundaries and a six.
India 'A' started their essay on a poor note, losing opener and Team India discard Gautam Gambhir (10) in the fifth over and that was a bad omen. India lost wickets at crucial junctures and the Australian pace trio of Mitchell Johnson, Shaun Tait and Shane Watson nipped in the bud any prospect of such a partnership.
Opener Robin Uthappa (50) looked both solid and aggressive during his 57-ball knock but Watson plotted his peril catching the batsman off his own bowling.
To make it worse, TP Singh (17) and Venugopal Rao (19) fell in quick succession before S Badrinath (59) and Rohit Sharma (41) tried to stem the rot with a 68-run fourth wicket partnership but Watson again thwarted the move, removing Rohit.
Just when he looked set for a big knock, India's man-in-form Badrinath was caught by Jaques off Tait and the next delivery saw Piyush Chawla being trapped for a nought and Tait was on a hat-trick.
The milestone, however, eluded the Australian as he strayed the delivery on the leg and conceded a bye run and India 'A' ended the day on 221 for seven in 64 overs -- still 240 runs behind the hosts.
Parthiv Patel was not out on 18 and giving him company was RP Singh on one.
Brief score: AUS A 461 for 4 declared (Phil Jaques 240, Travis Birt 130) IND A 221 for seven (Robin Uthappa 50, S Badrinath 59, Rohit Sharma 41, Shane Watson 3/39).