The match was their second meeting in the competition and the champions who had earlier thrashed their opponent 5-0 in the group matches was stretched to the limit by the rejuvenated side until the final whistle.
Cebagoo had a dream start when they opened their scoring as early as in the 11th minute through Md Nizam Jifferi with a tap in from a pass by Marwan Kadir.
Marwan then turned scorer and doubled their lead in the 35th minute with a superb long range dipping shot outside the penalty box.
The second half saw the more experienced Beverly FC coached by former state great Awang Sabtu played with more urgency and attacked their opponent's from the restart.
Cebagoo without their influential player Shahrudin Yakuub who is now playing for the state senior team were in all sort of problems.
They were on the back foot for most of the second half and have their custodian Sukree Jamlih to thank for as he managed to thwart several dangerous attempts to maintain their advantage.
However, he had no answer in the 63rd minute when the lively Mardoni Saini displayed his neat skill to get pass the last defender before shooting across the keeper and into the far right corner.
The goal further boosted the team's confidence as they increased their tempo and tried to find the equaliser with more attempts on goal.
They even had a goal from a free kick disallowed later in the half after the referee decided that there was an earlier infringement.
Beverly's Rezuan Khan Aman also had a powerful shot missed the up right by a whisker towards the end of the match.
Despite their relentless attempts, the goal just refused to come and credit must also be given to the young Cebagoo players as they managed to hold firm to claim their first league title.
Cebagoo FC's patron Hj Mohd Joh Wid who was instrumental in the rise of the previously unheralded team was overjoyed with the result.
He praised the players, coaches and supporters for their immense inputs to the team's success.
"It was a fantastic result given that we faced a very strong senior team with bags of experience.
No doubt we have beaten them before but the final is a totally different game and I am pleased that our young team displayed a great character and managed to excel against all odds."
He also disclosed that the players who are all from the Sepanggar area will continue to train as a team.
"Our aim is to represent Sabah in the 2013 FAM cup therefore the team will remain intact and a selection trial will also be held soon to select 18 players below 23 years to beef up the squad."