The fixture, now in its second year, was played before the BBL clash between the Brisbane Heat and Perth Scorchers, featuring Australia's best male Under 19 cricketers ahead of the Australian squad's departure on Sunday for the ICC Under 19 Cricket World Cup in New Zealand.
The Ponting XI batted first, posting 3-153 from their 20 overs.
Sydney Sixers rookie Jack Edwards was the star, scoring 99 not out off just 60 deliveries.
He combined for a 48-run opening stand with Brisbane Heat and Queensland Bulls batsman Max Bryant (21), while NSW Blues rookie Param Uppal was unbeaten on 19 off 15 deliveries.
Fast bowler Jason Ralston (0-18 off four) was the pick of the Gilchrist XI bowlers.
In reply, the Gilchrist XI shared the load with the bat, with five players reaching double figures including captain Aaron Hardie (28) and opener Ryan Hackney (27).
South Australia rookie Lloyd Pope claimed 2-19 off four overs with his leg-spin, and the Ponting XI claimed two final-over wickets.
But a six off the second-last ball of the final over from Jarrod Freeman - his first ball at the crease - saw the Gilchrist XI home by three wickets.
For a full scorecard, visit www.cricket.com.au