Tore Andre Flo missed the crucial penalty, which required nine penalties a side before a winner could be decided. The match finished 0-0 on the night after extra time. with the first leg at Scunthorpe having been a 1-1 draw.
Scunthorpe will now face Millwall in the League One play-off Final at Wembley to decide who will join Town in the Championship next season.
Trotter's contract at Town expires at the end of the season. It's expected he will meet with manager Roy Keane after the play-off final at Wembley.
Click here for a rundown of Liam Trotter's season to date.