The sturdy Nigerians began cautiously and were evenly matched by Sikkim Police till the first half.
However, the visitors found their composure in the second half and Aigiojano Felix drew first blood in the 49th minute with a volley.
The second goal for the Nigerian team came with a dose of luck and Egaware Charles's long range shot was slipped by Sikkim Police goalkeeper into the net through his legs.
Oyoh Emmanuel then beat the offside trap and the Sikkim goalie with a neat placement in the 83rd minute to make it 3-0.
The Nigerian team now plays BJS, a Bangladesh football club, in the quarter-final on November 1.
The second pre-quarter final match between Punjab Police and Chittagong Abahon of Bangladesh ended in a goalless draw.
The extra-time was called off due to bad light and will be played tomorrow.
Bhutan XI and Tibetan National Football Academy clash tomorrow for a berth in the last eight.
Nigerian Eagles vs Sikkim Police 3-0