In an insignificant match, Kerala took the lead in the 31st minute through Mohammed Sameer whose 35-yards left footer beat rival keeper Enborlang Nongtdu to find the far post.
They increased the lead seven minutes before the end when Mudbun Wilwet shot home from inside the box after Sabir S did the spadework on the left.
Meghalaya, who came with counter moves, also had their chances to score but Shachin Khongsit and Dan Mukhim failed to get past the rival goalkeeper Irfan Mohammed.
Thus, Kerala and Meghalaya, who have completed their league engagements, finished third and fourth with four and zero points respectively.