After failing to register successes from two previous finals, Vipers finally had the last laugh in the 42nd edition of the annual knockout competition at the expense of a newly promoted side.
Midfielder Pius Wangi doubled the advantage a minute to the half hour mark before Onduparaka's Gadaffi Wahabu reduced the deficit with a curling shot from a free-kick in the 38th minute as the half time ended in favour of Vipers.
Upon resumption, either side called for changes minutes after the second half started.
Rashid Agau replaced Ajobe Toto for Onduparaka and Mutyaba paved way for the lanky Alfred Leku.
In the 58th minute, Wangi scored Vipers' third, his second on the day - a beautiful left footed finish into the roof of the net from a melee.
Yamandu Tawakal had an attempt from distance kiss the goal post and sailed out as Onduparaka, who eliminated last year's champions, SC Villa staged a gallant fight.
Ssekisambu has now won the trophy for the third year running with three different clubs (URA, SC Villa and now Vipers) while Vipers' coach, George 'Best' Nsiimbe earns his second title as coach having won the tournament with Victors.
For the second time in a row, Ssekisambu was named the Most Valuable Player of the tournament as Vipers SC joins the long list of winners since 1971, and the ticket to represent Uganda in next year’s CAF Confederation Cup.
Most Valuable Player: Erisa Ssekisambu (Vipers)
Top Scorer: Muhammed Shaban (7 Goals) – Onduparaka
Best Coach: George 'Best' Nsiimbe (Vipers)
Best Goalkeeper: Isma Watenga (Vipers)
Presidential Award: Lawrence Mulindwa
Fair-play: Onduparaka Medical Team