The Imps lost 3-1 at Exeter in the play off semi final second leg, denying them a second trip to Wembley this year.
It followed a goaless draw at Sincil Bank last weekend.
That means they miss out on promotion and must prepare for a second season in League 2.
City went behind in the 27th minute and never really recovered conceding 2 more goals in the second half.
Matt Green's strike for the Imps 12 minutes from time proved to be just a consolation.
The final whistle saw some Exeter fans invade the pitch and reports of violence.
There are claims Lincoln's 78 year old kit man was assaulted and Nicky Cowley was punched in the head.