Fleetwood were trailing 3-1 from the first leg but Jon Parkin's goal in the final minute came too late to prevent the Spireites from setting up a meeting with Peterborough at Wembley on Sunday March 30.
It comes two years after Chesterfield beat Swindon in the showpiece final to lift the trophy for the first time.
Fleetwood flew at Chesterfield from the first whistle and Parkin shot narrowly wide in the first two minutes, but the home side had chances to increase their advantage before half-time.
Jimmy Ryan forced Chris Maxwell to beat out a stinging drive in the 19th minute and the goalkeeper also turned over a Marc Richards header and kept out a Jay O'Shea shot.
The visitors kept pressing in the second half and Antoni Sarcevic went close in the 73rd minute when he cut across the area and unleashed a goalbound shot which hit Liam Cooper.
Chesterfield had a great chance to finish it when Gary Roberts crossed from the left but Eoin Doyle headed over from six yards and Fleetwood kept the tie alive with a goal from Parkin in the 90th minute, the big striker turning in a cross from the left.
However, despite six minutes of stoppage time, Chesterfield held on to triumph 3-2 on aggregate and book their place at Wembley.