EXETER City slipped out of the play-off places in League Two after they fell to their fifth defeat at St James's Park this season.
Again it was a set-piece which proved to be City's undoing as Rotherham United's captain Ian Sharps headed the Millers into a first-half lead.
City boss Paul Tisdale admitted he was disappointed after the game at having given the Millers a head start, but added that he was satisfied with the players' performances.
"I'm disappointed we have lost, but I'm not too unhappy with the way we have competed," said Tisdale.
"It becomes very difficult when you concede the first goal and that has happened too often."
In the rainy conditions it was a credit to the City ground staff that the game was given the go-ahead, but the conditions suited the South Yorkshire side better.
Alan Gow, who has been instrumental in Exeter City's revival, struggled to run with the ball due to the excess surface water and the close attentions of the Rotherham United midfielders.
It was the Millers who went closest to breaking the deadlock early on as a lively Ben Pringle threaded a ball through to Alex Revell in the area. However, at angle, he could only drive a shot against the legs of Krysiak, who stood tall at his near post.
City hit back as Jamie Cureton and Gow both tested Andy Warrington with shots from inside the box. Then Gow produced a moment of magic as he side-stepped his marker and curled a 25-yard shot against the crossbar.
But it was Rotherham who ended the half on top and when Krysiak was forced to tip an Revell header over his crossbar, from a corner, the warning signs were there. Then, with the next cross into the box, Sharps rose above his markers, at the near post, to glance a header home.
Exeter City enjoyed the greater possession after the break, but they were unable to get up any head of steam as Rotherham took to time-wasting tactics as early as the 47th minute.
O'Flynn, who had impressed in recent home matches against Fleetwood and Wimbledon, was introduced to the action, but despite getting into a couple of good crossing positions he couldn't deliver a telling final ball.
Gow tried a shot from distance. Warrington spilt the shot in the slippery conditions but, with Cureton lurking, Sharps was in the right place to boot the ball to safety.
At this point Rotherham were getting plenty of men behind the ball.
City's rhythm was also disrupted by injuries, with Steve Tully limping off to join an already injured Tommy Doherty in the treatment room.
In the closing stages Rotherham's Mitchell Rose was sent-off for a two-footed challenge on Aaron Dawson, but by that stage the Millers had done just about enough to see out the match.
Tisdale was pleased with the efforts of his players even if he admits the approach in the second half didn't quite pay-off.
"You have to, I suppose, go one way or the other," he said. "You either go completely route one and push the opposition or you pass the ball and try and pick them off.
"In the past we have tried to pick teams off, but (against Rotherham) we have gone a little bit more direct and forceful. It didn't work either, but we certainly had a real go at it.
"I'm finding it very hard to criticise the players' effort and commitment."