Holmes was originally named in the No. 1 jersey when team lists were released on Tuesday.
Dugan will now start the match in the fullback position, with Holmes moving out to the wing to replace the injured Sione Katoa.
Aaron Gray will then shift from the wing into the centres.
Flanagan has said that it’s likely Dugan and Holmes will share the fullback role though during the local derby with rivals St George Illawarra.
The game will be the first the match-up for Dugan against his old club.
Dugan left the Dragons at the end of 2017, with St George Illawarra not willing to pay Dugan fullback money to play in the centres.