The Owls looked jaded and short on ideas going forward and were sloppy at the back.
With the playoff contenders elsewhere in good form, a second round of dropped points inside a few days feels like a knock, though they were helped as results elsewhere went their way.
Here are our player ratings on a difficult afternoon in Kent.
1. Owls Callum Paterson battling away Pic Steve Ellis
Owls Callum Paterson battling away Pic Steve Ellis Photo: Steve Ellis
2. Bailey Peacock-Farrell - 7
Made some important saves, most notably a double stop in the first half, and kept Wednesday in it when Gillingham were at their best. Photo: Steve Ellis
3. Jordan Storey - 6
Gave a good account of himself. Won headers and read the game well but was involved in a mix-up or two early doors. Photo: SWFC
4. Chey Dunkley - 4
Playing his first match for 79 days, he had an important role adding physicality and organisation to the Owls defence. Picked up a yellow after hesitation early doors and looked a long way off the pace for most of the match. Photo: Steve Ellis