Adam Le Fondre was perfectly placed to nod home a rebound on the brink of half-time and double his tally for the tie after his goal had given the Millers a 1-0 first-leg advantage on Saturday.
And Kevin Ellison made sure of their place in the final when he thumped home a header from close range with 22 minutes remaining.
Aldershot's attempts to get back into the game were snuffed out by a solid Rotherham defence and Kevin Dillon's men were left to rue several missed opportunities in the first leg.
The win for Rotherham sets up a likely final with Dagenham and ensures a first appearance at Wembley since their 1996 Football League Trophy success.
The Millers had not won at Don Valley Stadium since the end of March but they settled the quickest, forcing a succession of early corners.
But they could not create any clear chances and as the first half wore on, Aldershot began to get a foothold in the game, with Dean Morgan wasting a good opportunity when he blazed over from the edge of the area.
The game really began to open up and Aldershot felt they should have had a penalty when Dave Winfield went down under a heavy challenge, but Rotherham also threatened when Le Fondre's cross-shot glanced off the top of the bar.
With the Millers having scored just four times in their last nine games, the first goal was always going to be crucial and it was Ronnie Moore's side that broke the deadlock at the perfect time, with just two minutes of the first half remaining.
Shots keeper Mikhael Jamiez-Ruiz could only palm the ball out when a deep Nicky Law corner was headed back across goal by Ian Sharps, and Le Fondre was in the right place to nod home from close range.
It was the prolific striker's 30th goal of the season and it doubled Rotherham's aggregate lead.
Aldershot had to come out firing in the second period if they harboured any hopes of turning the tie around, but it was Rotherham who almost extended their lead further.
A superb piece of skill saw Ryan Taylor break free of his marker and his low drive was well saved by Jaime-Ruiz.
Aldershot were pushing forward in search of a way back into the tie but they came up against a stern home side, who were also dangerous on the break.
Neither Ellison or Taylor were unable to get on the end of a threatening Law cross after Le Fondre had set him clear, while Le Fondre's drive was deflected just over.
The Shots eventually got in behind Rotherham and should have levelled on the night but Morgan put his effort way over at the far post.
And the Millers immediately took advantage as they went up to the other end and extended their lead. The influential Law broke the offside trap and teed up Ellison, who made no mistake with his header from six yards.
An inevitable bout of Aldershot pressure came with Andy Warrington palming away Aaron Brown's effort and Gavin Gunning clearing off the line as the Millers held firm.