The Millers, who will now face Leyton Orient in the final on May 25, had Ben Pringle to thank after he laid on two goals to send the hosts to the final at Wembley.
Rotherham did fall behind when Preston opened the scoring after 16 minutes, but goals from Wes Thomas, Lee Frecklington and the prolific Kieran Agard completed the comeback.
Preston went ahead when Paul Gallagher's deep free-kick from the left evaded everyone in the box, including Rotherham keeper Adam Collin, before the ball bounced in the six-yard box and up into the top corner of Collin's net.
But the hosts were level just eight minutes later through Thomas' powerful header, from an almost identical delivery.
Pringle's set-piece was whipped in from the left and Thomas was on the move to get across his marker and powerfully head past Declan Rudd.
And 10 minutes later Rotherham turned the game on its head through a brilliant downward header from Frecklington.
Pringle, whose wicked deliveries were a feature all night, whipped in another stunning ball from the left wing and Frecklington rose majestically to head in off the post from 14 yards.
However, all the hosts' good work was almost undone just before the break when Collin spilled a long-range strike from John Welsh, but fortunately for the Millers' keeper his luck was in, as the ball dropped wide of the post.
Pringle, whose efforts deserved a goal, came close to making it 3-1 five minutes after the restart when his thumping left-foot volley smashed against the crossbar and away to safety.
But Preston were quick to offer a response and after Gallagher was afforded too much time and space in midfield he fired over a deep cross, which first-leg hero Joe Garner volleyed over the bar.
The hour mark passed and this time Gallagher was the culprit as he headed wide after a good cross from the right from the sub Chris Humphrey.
But Rotherham put the seal on their victory with 67 minutes on the clock through Agard's 26th goal of the season.
James Tavernier turned Bailey Wright inside out on the right wing and then intelligently pulled the ball back for Agard to clip a shot in off the far post to send the New York Stadium into raptures.
Preston, to their credit, still offered an attacking threat and Jack King's speculative strike deflected off Kari Arnason and against the post as Rotherham fans held their breath.
And when Garner hit the upright via another deflection with 10 minutes remaining, Preston knew it was not going to be their night.