A second game in three days against physical, committed opposition proved too much for the Millers who could have no complaints at their eight match unbeaten run in the league being ended.
Behind early on, they were clearly below par.
And Vale, showing the greater all-round commitment and desire, deservedly got the better of them.
However, once again the Millers found themselves debating a critical refereeing decision.
This one involved the 54th minute dismissal of Claude Davis for which the club is to launch an appeal.
Millers boss Steve Evans said the reaction of former Millers striker Tom Pope was “disgraceful” and resulted in Davis being shown the red card.
Pope, having been fouled, was lying over the ball and Davis clearly toe-poked it from under him.
Pope reacted as if in pain, rolling in apparent agony which suggested he’d been kicked.
“Why was he rolling about like that?” asked Evans.
“It was nothing short of disgraceful for one professional to do that to another.
“The fourth official told us what he had seen and that it definitely wasn’t a red card. We will appeal it.
“What I’d like to know is why there wasn’t a red card for our penalty?
“That was a clear goal-scoring opportunity which we were denied and should have been a red.”
However, Evans admitted that his side had not played well but added that Craig Morgan and Alex Revell had played despite illness.
“But whilst we were disrupted, there are no excuses.
“Port Vale played quite well but we finish the year in a play-off spot and that ain’t bad.”
To compound Rotherham’s match-day misery, the DVD showed Vale’s second goal was offside.
Also, Ben Pringle will be suspended and will be absent for the New Year’s Day home game with Coventry City, for a fifth booking after he wellied the ball high over the stand.
Things began to go wrong before kick off when Lee Frecklington - outstanding in the win at Bradford City - fell ill during the warm-up, got worse and had to pull out.
Davis, on the bench in the side originally named, was brought in.
The Millers were already without Mark Bradley and Rob Milsom through one-match bans.
So, James Tavernier switched to right back, Joe Skarz returning at left back.
There was a return for Michael O’Connor in midfield but he struggled to make an impact.
Rotherham seemed to be caught cold at the start and Pope might have notched in just three minutes. His header was too close to Collin.
Pope’s duel with Davis was nothing less than robust and pretty close to all-in wrestling at times but nevertheless than an interesting contest to watch.
Pope had an assist in Vale’s goal on eight minutes.
He got a flick on to a long ball and Louis Dodds came in off the right flank, moved across the face of the area and struck a shot past Adam Collin.
It needed the quickest of recovery runs by James Tavernier to stop ex-Owls midfielder Chris Lines breaking clean through and it was the sort of breakaway goal which Vale utilised to such deadly effect in last season’s 6-2 defeat of the Millers.
Tavernier began the move which ended with him being brought down for the penalty after a link with Agard.
The Millers’ top scorer switched sides from his last penalty but Sam Johnson got across to his right to make the save.
It meant that for the first time in an away game - and they’d won their last four away in the league - since the defeat at Leyton Orient at the end of October, Rotherham were asked to chase the game.
Against a tough, organised and physical defence like Vale, it is a difficult ask and every inch had to be fought for as the Millers strove to assert themselves.
Opportunities were scarce and Arnason, striding through midfield, took responsibility himself and struck a fierce 30 yard effort which was not far wide.
Loft, in a floating role, struck an effort close and then saw a shot deflected not far over.
Pope had the ball in the net straight at half-time but the offside flag was up and on 54 minutes came the moment of controversy with Rotherham being reduced to ten men.
Pope was fouled by Davis near the touchline and laid on top of the ball.
Davis didn’t need to do it - and shouldn’t have done - but he toe-poked the ball out of play from under Pope whose complete over-reaction made it appear that he’d been kicked.
Davis clearly kicked the ball and if Davis’s shin did make any contact with Pope, it hardly seemed worthy of such a reaction from the ex-Millers striker.
But it convinced the man who mattered.
The referee took his time before showing red and matters ended with Rotherham’s management duo indicating that the fourth official might have thought it was an error.
However, whilst there was obviously no malicious intent, the whistle had gone for a foul and there was no need for the Millers’ defender to do anything other than prepare for the free-kick.
Rotherham were up against it and more so on 67 minutes with Vale’s second which effectively killed Rotherham’s hopes of getting anything out of the game.
The ball was played towards Pope but his mere presence was enough.
It simply went through, untouched, into space and Gavin Tomlin, seemingly offside, swooped to fire home.
The remainder of the game was about Rotherham trying to salvage something and Vale breaking out but somehow failing to finish several attacks when they had a man advantage.
Rotherham got no joy at all out of Vale centre backs Richard Duffy and Liam Chilvers who won everything.
It wasn’t until the closing minutes that Rotherham had a really threatening effort with Tavernier firing just over and Agard bring a fine save from Johnson.