Winger Joe, who arrived from Wigan at the Roosters in the off-season, will play in the tournament for the first time.
Prop Thomas will also feature in Auckland for South Sydney for the first time after missing the cut last year. Twin brother George was in the Rabbitohs team for 2015, which won the competition, but has not been selected this year.
Older brother Luke Burgess was not picked by Manly.
The Nines take place at Eden Park this weekend.