Yorkshire batsman Ballance's knock of 104 from 154 balls included 16 fours and one six as the Lions closed on 269 for seven with spinner Nathan Lyon the pick of the Australia bowlers with three for 80.
Worcestershire all-rounder Moeen Ali also contributed 61 off 101 deliveries, but with bad weather forecast for Saturday the tourists' hopes for batting practice in this match could well be frustrated.
Rain fell on and off throughout the morning, meaning there was no play before lunch with conditions only clearing up in time for play to start at 2pm.
England Lions won the toss and chose to bat but they lost Luke Wells for 10 in the sixth over when he edged James Faulkner to Australia wicketkeeper Matthew Wade.
His fellow opener Alex Lees should have followed on 16 but the tourists' captain Shane Watson put down a straightforward chance at slip, off Lyon.
Fortunately for Watson, his mistake only cost 17 runs as he pouched his next opportunity at first slip after Yorkshire's Lees edged another Lyon delivery to walk for 33.
The Lions' captain, Eoin Morgan, was to make only five before throwing his wicket away with an ugly slash off Lyon to Watson, again at first slip.
However, Moeen was to complete a confident half-century off 85 balls as the hosts reached lunch on 156 for three with runs coming easily.
But Moeen perished in the fourth over of the evening session when he was taken by Steve Smith at second slip off Mitchell Starc to break a fourth-wicket partnership of 70 with Ballance.
Ballance, whose previous tons came for Yorkshire against Warwickshire and the Unicorns, then went past 50 off 90 deliveries.
Lyon was brought back into the attack in the 56th over and with his first ball forced Ben Stokes to edge to Watson at slip and fall on 19.
Lions' wicketkeeper Jos Buttler (7) went cheaply by smashing Smith's waist-high full toss straight to Lyon at deep midwicket.
Ballance then surged past 100 from 153 deliveries by hammering Smith for six over midwicket, only for the part-time spinner to trap him lbw with the very next ball.
Keith Barker and Liam Plunkett then survived the final four overs and will resume on nine and five respectively.
- Sports & Recreation
- Shane Watson
- England Lions
- Moeen Ali