Simeon Jackson was the hero when he buried a header from a Josh Wright corner as the game looked destined for extra time.
Gillingham dominated the first half and were only kept at bay by the outstanding Luke Daniels in the Shrewsbury net, but Paul Simpson's side improved after the break and looked the more likely to break the deadlock.
But Gillingham mounted one last attack and when they fortuitously won a corner, Jackson was left free to squeeze a header in between full-back Neil Ashton and the post and send the Gills back into League One.
The club's Priestfield stadium will welcome the likes of Leeds, Southampton and local side Charlton next season and Stimson is looking forward to the challenge.
He said: "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."
Stimson admitted Jackson could become a transfer target for bigger clubs after his match-winning performance but is confident of keeping him in Kent.
He said: "He's a goalscorer. He's got 21 goals now but we have not had one phonecall about him.
"I'm sure managers have watched him this season but he would cost a lot of money.
"He might need another year before he can play in the Championship so I am confident we can keep hold of him.
"When the opportunity came up he was on hand to score and he deserves all the praise in the world.
"He's a serious pro and always wants to improve. Hopefully he can take this club forward."
Shrewsbury boss Simpson refused to dwell on the reward of the decisive late corner and challenged his players to come back stronger next season for another promotion challenge.
Television replays showed the corner should not have been given as the ball went out off Gills winger Andy Barcham but Simpson admitted his side were ultimately beaten by the better team.
He 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.
"We must get stronger and make everyone better for it.
"We didn't play as well as we could have done and gave the ball away too often and came up short.
"We had some half chances but over the 90 minutes they passed the ball better and created the better opportunities."