After both sides failed to break the ice in regulation time, Thoiba struck from the spot in the 116th minute to earn Manipur a hard-fought victory at the Nehru stadium.
It was Manipur who dictated the terms right from the outset and could have taken the lead at the stroke of halftime, only for Tikem Singh to squander two sitters.
Manipur continued to pile on the pressure and came close to breaking the deadlock again but an alert Services goalkeeper Robikanta Singh kept them at bay with some fine saves.
During extra-time Manipur again dominated with their players missing several chances with Tikem Singh and Jimmy Singh getting the best of them to win the game for the former champions.
Manipur finally reaped reward for their consistent forrays when Services defender P Sumesh was caught handling the ball. Thoiba then stepped on to deliver the knock-out blow to put Manipur through.
