Fans were on tenterhooks during the 90s minutes of superb football which ended in a penalty kick out.
City were behind one nil and then by two one but fought back twice resulting in two goals each for both teams.
Blues men Kyle Rock and Andy McAlinden scored a goal each for Craigavon City FC.
And the bid for the Alan Wilson Cup went to penalties.
All four penalties taken by City players were scored.
Captain Johnny Cochrane was first up, followed by Andy McAlinden, Kyle Rock and Conor McKavanagh took the final and winning penalty kick.
The win comes just weeks after one of Craigavon City FC’s founding fathers John Cochrane died.
One fan said: “A fantastic win for Craigavon and, on the back of John Cochrane’s death, it was a very emotional night.”
The club was set up in 2007 in Craigavon and this is the first time in their short history that they have won the Alan Wilson Cup.
After a long weekend of celebrations, Craigavon City FC said this week: “Now that the dust is settling and the cobwebs are shaking off we would like to send out a massive thank you to two special sponsors that have supported us through thick and thin over the past few years.
“Drumgor Tavern Bar and Off Sales - these guys hosted the cup champions over the weekend and always support our players staff and community with warm welcomes. Massive thank you guys for all the help up to now and going forward.
“Unison Craigavon Hospital Branch - our main sponsors of the first team and great supporters of the club and all of the fundraising we do. Without these guys we would not be where we are today so a massive thank you to Unison.
“As always folks please support our local sponsors and businesses in these hard times.”