Comer hit 1-2 after the break with Paul Conroy increasingly influential in midfield as Galway outscored the hosts 1-10 to 0-3.
Fermanagh captain Eoin Donnelly was black-carded after nine minutes yet Pete McGrath’s side were worthy of their 0-7 to 0-3 half-time lead. But it was all Galway after the break.
Comer and Paul Conroy led the way while Barry McHugh nailed 0-4 from frees.
Galway manager Kevin Walsh was pleased, but not ecstatic.
“It’s important to get structures right and sometimes results don’t show that. We’re happy with the points today but we’re not celebrating victories or mourning losses. Win or lose, you have to treat it the same way.”
Eddie Courtney showed well inside and clipped over two early points for Fermanagh before Galway drew level through Michael Daly and a long-range effort from Conroy.
From three points all, Fermanagh took over in the 10 minutes before the interval with four points in a row, three from Sean Quigley.
Galway stormed back and left their hosts shell-shocked on the restart.
Comer had the ball in the back of the net after just 10 seconds to undo most of Fermanagh’s good first-half work.
Fermanagh tried to keep their noses in front as long as possible and Barry Mulrone scored a neat point from the wing, and Corrigan again edged them ahead after Galway drew level, but the tide was turning. Two successive points from Michael Daly put the visitors ahead for the first time, at 1-7 to 0-9 in the 54th minute.
They kicked strongly for home, with Barry McHugh nailing three frees into a tricky wind and Conroy winning a kickout, running through and clipping it over the bar.
Fermanagh had a strong penalty claim turned down in the 67th minute when Declan Kyne appeared to pick the ball up off the ground, but Galway were already five points up and looking convincing.
Erne cornerback Cian McManus got a straight red for a body punch on Gareth Bradshaw near the end, but it was irrelevant to the result.
S Quigley 0-3 (1f, one ‘45’), T Corrigan 0-2 (1f), E Courtney 0-2, B Mulrone, L Cullen, A Breen 0-1 each.
D Comer 1-2, B McHugh 0-4 (4f), M Daly 0-3, P Conroy 0-2, T Flynn, E Brannigan 0-1 each.
C Snow; P Rehill, C Cullen, C McManus; D McCusker, R McCluskey, B Mulrone; E Donnelly, L Cullen; A Breen, C Beacom, P McCusker; E Courtney, S Quigley, T Corrigan.
R Lyons for Donnelly (BC, 9), C Corrigan for Beacom (HT), D Keenan for P McCusker (59).
R Lavelle; D Kyne, D Walsh, L Burke; G O’Donnell, G Bradshaw, J Heaney; P Conroy, F O Curraoin; T Flynn, D Comer, M Daly; C McDaid, B McHugh, S Armstrong.
E Brannigan for Armstrong (41), S Kelly for McDaid (42), E Tierney for McDaid (70), C Sweeney for McHugh (70).
Jerome Henry (Mayo)