Speedster Stanlake has been released from the Australian ODI team and is the only change to the side that defeated the Melbourne Stars by 41 runs last night.
Travis Head will again lead his side before the Domain Test Series against Sri Lanka beginning January 24.
The Strikers captain became the first player to reach 1,000 BBL runs for the club in his 43 (31) against the Stars, within a crucial 74-run partnership with Colin Ingram.
Ingram was named Player of the Match for his 57 (41), in what was his second half-century of the season.
Ben Laughlin was also impressive on his return from injury with figures of 3/19, the leading Big Bash wicket-taker extended his tally to 90.
Australian vice-captain Alex Carey and Peter Siddle remain unavailable for selection as they are in the XI for the Gillette One-Day International Series against India starting today.
Tomorrow's clash at Spotless Stadium begins at 2:15pm (ACDT), and will be broadcast on Fox Cricket.
The final XI will be announced at the bat flip.
BBL squad v Sydney Thunder
Travis Head (c)
Harry Nielsen (wk)
In: Billy Stanlake
Out: Wes Agar