Comer came off the bench to make the difference against Sligo in the semi-final, scoring two points and creating the late goal for Rob Finnerty that sank Sligo.
Maher missed the Sligo game but is named at centre-forward as Jack McCabe and Liam Ó Conghaile revert to the replacements where Matthew Tierney has returned to after missing out since the league game against Tyrone through injury.
Meanwhile Galway hurlers make three changes, bringing in Jack Grealish, Evan Niland and Gearoid McInerney for their Leinster SHC trip to Wexford tomorrow.
From the Kilkenny game last weekend, David Burke, Sean Linnane and Darren Morrissey drop out.
Galway (SF v Mayo): C Gleeson; J McGrath, S Fitzgerald, J Glynn; D McHugh, J Daly, L Silke; P Conroy, S Kelly; J Heaney, J Maher, C Darcy; R Finnerty, D Comer, S Walsh. Subs: C Flaherty, S Mulkerrin, E Kelly, D O’Flaherty, J McCabe, C Sweeney, K Molloy, L Ó Conghaile, C Ó Curraoin, M Tierney, S O’Neill.
Galway (SH v Wexford): D Fahy; J Grealish, Daithi Burke, F Burke; G McInerney, P Mannion, C Fahy; R Glennon, G Lee; T Monaghan, E Niland, B Concannon; C Whelan, C Cooney, C Mannion. Subs: E Murphy, A Tuohey, S Linnane, E Lawless, D O’Shea, David Burke, J Glynn, Joseph Cooney, John Cooney, J Flynn, D McLoughlin
Waterford (SH v Tipperary): S O’Brien; K Bennett, C Prunty, I Daly; M Fitzgerald, T De Burca, C Lyons; J Barron, D Lyons; N Montgomery, Stephen Bennett, J Prendergast; D Hutchinson, M Kiely, K Mahony. Subs: B Nolan, I Kenny, J Fagan, M Power, P Curran, Patrick Fitzgerald, Shane Bennett, P Hogan, Padraig Fitzgerald, P Leavey, T Barron.
Tipperary (SH v Waterford): B Hogan; J Ryan, R Maher, C Morgan; M Breen, B O’Mara, C Bowe; W Connors, E Connolly; A Tynan, G O’Connor, J Forde; J Morris, M Kehoe, S Hayes. Subs: R Shelly, C Barrett, P Cadell, S Kenneally, P Maher, D McCormack, J McGrath, N McGrath, A Oromonde, C Stakelum, D Stakelum