Rovers' last gasp winner sees Stancliffe's men leapfrog South Yorkshire rivals.
A last minute penalty ensured Doncaster came away with all three points following their action packed encounter with Rotherham at Cantley Park.
Rovers came out 3-2 winners on the day, in a game which was not short of controversy.
The game saw Rovers take the lead twice, before being pegged back on both occasions by inform Millers striker Joshua Kayode.
However there was still time for Rovers to snatch the game right at the death, through midfielder Jacob Fletcher’s spot kick.
Rotherham had the opportunity to go 2-1 up in the game early on in the second half, but Reece McGinely’s spot kick was expertly saved by Rovers keeper James Leverton.
The game started well for the home side, and it took just five minutes for Rovers to go in front. A neat turn from striker James Morris allowed him space to fire a shot into the bottom corner, past the helpless keepers reach.
Rovers continued their dominance throughout the first half, Matthew Overton was next to try his luck following good work down the left hand side but Rotherham goalkeeper Harry Fidler, had little trouble pushing his effort over the bar.
The visitors began to a get a foothold in the game as the first half went on. Kayode, who was a constant threat throughout headed narrowly wide of Keeper James Leverton’s goal as the pressure began to grow.
The game sparked into life in the second half, with two goals and a penalty awarded by the referee in the space five minutes.
Firstly, Kayode clinically converted a deep corner with a superb header back across the face of goal to equalise for the Millers.
Just seconds later Rotherham were awarded a penalty with the chance to go ahead, but Reece McGinley couldn’t take advantage as his effort was saved by the diving Leverton.
Following the penalty miss, Rovers broke quickly, and after a foul prevented the counter attack, the consequent free-kick from Danny Amos was turned in from close range by striker Lloyd Henderson to put Doncaster back in front.
Rotherham did provide a constant threat throughout the second half, despite manager Paul Stancliffe saying he never felt his team were in danger of losing the game.
The Millers came into the game on the back of three consecutive victories, and their confidence was showing.
Both wide men were providing excellent width for the team, supplying talisman Kayode expertly, he blew another opportunity as he saw his low drive fizz just wide of the target.
It wasn’t until the 88th minute until Rotherham equalised for the second time in the game.
Once again a deep floated ball into the box was not dealt with and Kayode was on hand to tap in for the visitors.
The drama wasn’t finished there, as substitute Gooden Iyrwah drove into the Millers penalty box late on and was brought down, the referee had no choice but to point to the spot.
Midfielder Jacob Fletcher tucked the spot kick away, as Rovers made it seven points out of nine in the league.
Paul Stancliffe also reflected after the game that he was pleased with the performance and said all the efforts he had put into training have paid off.
“Certain things that we worked on in training we put into practice, and it paid off, I was pleased all round.
“I wouldn’t say we dominated the game, but we would have been unlucky to draw the game, we played well and I’m very happy especially after they equalised late on.”
That result sees Rovers leapfrog Rotherham in the Youth Alliance table, sending the Millers into 9th position on 15 points while Stancliffe’s side are up to 8th, level on points (16) with Chesterfield.