The Hive travelled for last Saturday’s game with only 14 players, and two of the squad were carrying injuries with another player struggling with flu.
Two Hermes goals from Andrew Courage before the 20-minute mark had Stonehaven on the back foot.
Although Danny Anderson hit a superb goal to reduce the leeway, the Hive were hit with another blow shortly afterwards when Neal McTavish was controversially sent off.
It was ten-a-side when Hermes had forward David Stevenson sent off late on, but with Stonehaven looking the likelier to score, Hermes wrapped it up with a last-minute goal from Michael Dawson.
“We started quite well, then they hit us with those two goals,” the Stonehaven assistant manager Jim George said.
“Danny Anderson then got us back in the game, cutting inside and hitting a left-foot screamer into the net – unusually for him, as he’s usually all right foot.
“Then came the sending-off. There was little in it, even the Hermes lad admitted that, as Neal and him tangled after a collision, but we had to take it on the chin.
“We played well with ten men, going for the equaliser – their keeper Lee Sweeney made a great save from Danny Anderson – then they scored with that breakaway in the last minute.
“I felt really sorry for the players as they worked their socks off.
“Defender Steven Reid, one of those carrying an injury, has been outstanding recently and had another great game.”
Stonehaven: Fraser Stark, Jonathon Millsom (Ryan Begg 63), Craig Lowden (Ryan Clark 74), Steven Reid, Neal McTavish, Rthys Gray (capt), Barry Smith, Ludwik Metelski, Danny Anderson, Craig Mackie (Michael Cormack 53), Robert Armstrong.
Stonehaven are scheduled to travel out to The Meadows to face Ellon United on Saturday, again in the McBookie.com Superleague (2pm), though the severe weather forecast means all games are in doubt this weekend.