In other big team news, Injury-hit Collingwood welcomed back Jeremy Howe among five changes, Richmond rested veteran Dion Prestia, and Melbourne forward Jacob van Rooyen was cut down by injury.
Gaff was dropped to the WAFL after tallying just four disposals in West Coast's season-opening loss to Port Adelaide, while former Greater Western Sydney big man Flynn was grounded on the eve of the season when he required hamstring surgery after a training mishap.
Flynn made a successful comeback last week and Gaff has been in hot form in the WAFL, convincing West Coast the time was right to bring the duo in for Saturday's clash with St Kilda at Optus Stadium.
The recall of Flynn will help ease the burden on the undersized Bailey Williams, who has retained his spot and is expected to play a bigger role in attack.
The Eagles have also recalled fit-again speedster Jack Petruccelle and defender Harry Edwards.
Defender Josh Rotham (illness) and Jayden Hunt (toe) were ruled out, while the axe fell on Tyrell Dewar and Jack Williams.
Struggling St Kilda have been boosted by the return of Tim Membrey, Hunter Clark and Dan Butler, but Liam Stocker goes out injured.
Howe has been recalled to bolster Collingwood for Friday night's clash with the Western Bulldogs, but the defending premiers lost Mason Cox, Brody Mihocek, Scott Pendlebury and Joe Richards to injury.
Oleg Markov, Jack Bytel, Ash Johnson and Finlay Macrae join Howe as inclusions.
Jeremy Howe will make a welcome return for Collingwood. (Morgan Hancock/AAP PHOTOS)
The Bulldogs recalled Rory Lobb to replace the injured Aaron Naughton among three changes, with Anthony Scott and Ed Richards ruled out due to concussion.
Hawthorn lost ruckman Lloyd Meek to an ankle injury for Saturday's match against Adelaide at the MCG, with his place taken by Ned Reeves.
The Crows go in unchanged.
Geelong brought in Gary Rohan and Mark O'Connor to replace suspended pair Mark Blicavs and Jhye Clark for Saturday night's clash with Richmond.
The injury-hit Tigers have rested Prestia, who joins Shai Bolton (concussion) on the sidelines.
Kaleb Smith will become Richmond's fifth debutant of the season, while  tough midfielder Jack Graham and Rhyan Mansell were recalled after recovering from injury.
Richmond have recalled Rhyan Mansell after injury. (Jono Searle/AAP PHOTOS)
Melbourne forward Van Rooyen is expected to only miss one week with an adductor injury, with Ben Brown a chance to take his spot for Sunday's encounter with Fremantle in Alice Springs.
The Dockers are likely to regain Michael Frederick from concussion, while Michael Walters is in danger of being dropped after being named on the extended bench.
Gold Coast welcomed back Sam Flanders from illness for Sunday's home match against Essendon.
The Bombers are battling a virus outbreak, but at this stage they've only lost last week's debutant Nate Caddy to illness.
Essendon key forward Harrison Jones is in line for a recall after serving a one-week suspension.
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