The Irishman blew Rotherham's chance of taking a second-half lead when he hit a tame effort from the spot and was then sent off for violent conduct three minutes from the end.
The referee also took centre stage with a pair of decisions that baffled fans and players.
First he gave Vale a corner after eight minutes following a linesman's flag when it was clearly a goal-kick.
From the resulting corner, Michael Husbands headed in past keeper Gary Montgomery to put Vale in front.
Rotherham produced a spirited reply and might have levelled a minute later when young striker Will Hoskins dipped an angled shot over the bar.
But after 25 minutes it was Rotherham's chance to profit from another strange decision from the referee.
After 30 minutes Rotherham skipper Colin Murdock came close to putting his side in front but headed just over, and five minutes later when Murdock powered another header goalwards from an Andy Monkhouse corner, it was cleared off the line.
Hoskins did well to set up Monkhouse soon afterwards but the lanky winger screwed his shot wide.
Rotherham keeper Montgomery had to produce a sharp save to deny Mark Innes and he produced another great save to deny Husbands.
Rotherham blew a glorious chance in the 56th minute when Jonathan Forte was brought down in the area by Mark Goodlad but Keane hit the resulting spot-kick tamely and it was easily saved.
Keane was red carded three minutes from the end for violent conduct following an off-the-ball incident.