It was three precious points thrown away by Steve Evans' men and could prove vital at the end of the season.
Here's five things we learned from the match.
Substitutions change games for both sides
Trailing 1-0 and having been poor throughout the second half, Wednesday boss Stuart Gray gambled and through three attacking players on and it helped change the game. The subs provided more support to Atdhe Nuhiu in attack and they flooded the Millers area with bodies. One of the subs Caolan Lavery scored and when the Owls had seven minutes of injury time to play with they had men on the pitch capable of not only getting an equaliser but also a winner.
Evans' substitutions and tactical changes and they also had an affect, but in an adverse nature. His reluctance to bring fresh legs on in the middle of park proved costly as Wednesday flooded forward, there is an argument that the ineffective Connor Sammon was left on too long and leaving only Jordan Bowery up front for the lengthy added time only invited pressure on. It also meant the Millers were in no position to go for a win once Wednesday had equalised for a second time.
The Millers are showing worrying tendencies
There's no doubt that the Millers are showing worrying traits in recent weeks and the sort of things that are happening to them happen to teams who end up going down. To be winning 2-1 going into injury time and end up losing should be unthinkable for any team worth their salt. To allow Wednesday back into the game so late was criminal and the generosity of the defending for the two late goals was of epic proportions. Their tendency to concede quickfire game-changing goals has led to defeats in their last three matches and coupled with their inability to hold on to a lead, it is a worrying trend going into the final run-in.
The boot's on the other foot this season
So much of Rotherham's success over the last couple of years has been their enduring ability to go until the last whistle and rescue points, turning defeats into draws and draws into wins. Well, they have been getting a regular taste of their own medicine this season and it tastes pretty rotten. The Millers have conceded 14 goals between minutes 80 and 90, their most vulnerable period of games, equating to a lost 14 points. Those dropped points, or even just a fraction of them, are likely to have a massive bearing come May. Winning the game in the 90th minute and coming out on the losing side should never happen, but it wasn't necessarily a surprise.
Things can change in a matter of minutes
They say a week can be a long time in football but events at New York, coupled with what Wigan were up to at the DW Stadium, proved that so much can change in around 20 minutes. When both games - Rotherham's clash with the Owls and Wigan's derby with Bolton - entered injury time, results meant that the Millers were nine points clear of the relegation zone. Then fate dealt the Millers a cruel twist as the Latics earned a draw with the last kick before Wednesday's late show robbed them of three points to bring the gap back to five. There is a real sense of a massive swing in momentum after the last two Saturday's results and Malky Mackay's men will have taken a real boost from them.
However, the quick turnaround on Saturday highlights just how quickly things can change and despite the glumness of the last two weeks for Rotherham they still remain five points ahead of the relegation zone. With seven games left there is plenty of drama to come.
Football doesn't really matter
For all the anguish and heartache the late developments at New York brought on, those emotions paled into insignificance with news of the tragic death of a Millers supporter before kick-off and the serious illness of another in a separate incident. It's hard to forget sometimes but football will only ever be a game, which in effect is meaningless. The family of that fallen Millers fan are now having to comprehend how their loved one went to a football match and didn't come back.
