The Sixers were set a target of 158 runs after their cross-town rivals won the toss and elected to bat first.
Opener Josh Clarke top scored for the Thunder with 29 runs, and was ably supported by Jason Sangha who finished with 22.
Former Australian T20 international Ben Rohrer also chimed in with 11 runs for the home side.
Ben Manenti was the pick of the bowlers for the Sixers, finishing with figures of 2-21, while Alex Glendenning also picked up two wickets..
The Sixers Academy's run chase got off to a flying start courtesy of opening pair Justin Avendano (51) and James Crosthwaite (21).
However, the Sixers were unable to keep up the fast tempo, losing wickets in the final overs as the required run rate continued to climb.
The Sixers Academy eventually finished on 6-141 from their 20 overs, with Nathan McAndeew finishing with 3-24 for the Thunder.
Sixers XI: Crosthwaite, Avendeno, Edwards, Cahlin, Waugh, Holt, Chhibber, Glendenning, Manenti, O’Bierne, Malone.
Thunder XI: Clarke, Gaucie, Sangha, Rohrer, Green (C), Sams, Mortimer, Hunt, Gilkes, McAndrew, Copperfield.
October 26: vs Qalanders at Blacktown International Sports Park (11am)
October 31: vs Hurricanes at Blacktown International Sports Park (11am)