Gillingham 1 Shrewsbury Town 0
Simeon Jackson, the Gills' top scorer, got free at the back post to head home a Josh Wright corner for his 21st goal of the season and the Canadian will have scored few more priceless.
The first 20 minutes passed with little more than mild panic at either end, but slowly it was Gillingham who got a grip on the encounter even if their attacking threat was nullified by the Shrews defence.
Shrewsbury captain Graham Coughlan diverted a Nutter free-kick just past his own post, and from the corner Wright fired over the top.
Gillingham were almost in again when some smart play ended with Barry Fuller's cross being flicked on by Dennis Oli and Neil Moss tidied up well at the back post.
The Gills worked the next corner well as Andy Barcham left the ball for Nutter, whose powerful shot was diverted over the top by a combination of Grant Holt and goalkeeper Daniels.
Shrewsbury's first real effort came 10 minutes before the interval when former the former Shrimper centre-back Garry Richards fouled Nick Chadwick and Ben Davies - from fully 30 yards - sent the free-kick just wide.
But Daniels was at it again in stoppage time of the first half, diving low to his right to claw away a Wright shot through a crowd of players.
The second half started in a similar fashion as Barcham wriggled free and cut inside before unleashing a right-foot shot which was bound for the top corner, but Daniels pushed it away.
Gills and ex-Blue keeper Simon Royce made his first save of note not long after when a long Graham Coughlan free-kick was headed on by Kelvin Langmead for Davies to strike goalwards, but Royce clung on.
And Langmead caused problems with another towering header across goal, but Kevin McIntyre's diving header was horribly wide.
Shrewsbury were notably better after the break, and the game benefited for that, becoming a much more open contest.
A smart move gave Davies a clear run at goal, but his touch was heavy, allowing Barcham to get back and make a saving challenge, and Royce saved Langmead's header from the resulting corner.
However, after weathering the storm, the Gills took the lead from a Wright corner as the game fell into stoppage time. Jackson heading home despite the efforts of Ashton on the line.
Replays showed that the corner shouldn't have been given, but the Gills won't care!
The Shrews threw everyone forward and Davies crossed for Coughlan, but he headed over the top with Roycey scrambling, and the Gills held on.
Gills boss Mark Stimpson, yet another ex-player to wear the Blue shirt of Southend, said after the game: "It's massive financially. There are several local teams we can attract and with Leeds, Norwich and Southampton coming down we will have some big gates. We brought over 30,000 fans to Wembley today and we need to attract as many of them as we can every week. We had already arranged meetings with some players for next week regardless of what league we were going to be in. We need to improve the squad and we have to try and become a good League One side."
Shot stopper Simon Royce, speaking to the Echo, just focused on the match and didn't talk about whether he believed this was his last game for the club: "It was fantastic and just showed it was all about the day. We had given away nine goals in our two league games with Shrewsbury this season but this time we got a clean sheet and Jacko popped up with another goal."
Shews boss Paul Simpson, trying to hide his 'massive disappointment', said: "It wasn't a corner but if we look at things like that we will be clutching at straws. The referee had a decent game and if we deal with the corner then there's no problem. There are no words anyone can say in a situation like this. It's a horrible feeling and it's difficult but we have to pick ourselves up and move on. Football is a business which keeps evolving and we have to go back in on Monday morning and prepare for next season."
Gillingham: Royce, Fuller, Richards, King, Nutter, Lewis, Weston, Wright, Oli, Jackson, Barcham.
Subs Not Used: Julian, Bentley, Miller, McCammon, Jarrett.
Booked: Weston.
Goals: Jackson 90.
Shrewsbury: Daniels, Darren Moss, Langmead, Coughlan, Ashton, Humphrey (Ashikodi 90), Davies, Murray (Worrall 74), McIntyre, Holt, Chadwick (Riza 79).
Subs Not Used: Garner, Cansdell-Sherriff.
Booked: Coughlan, Murray, Holt.
Att: 53,706.
Ref: Clive Oliver (Northumberland).