Simon's shot hit the bar after he dribbled three opponents before Ekong scored from the rebound.
Sadiq Umar scored in the 56th minute to put Nigeria ahead against Guinea Bissau in their Group D encounter at the Africa Cup of Nations on Wednesday in Garoua, Cameroon.
He scored through an assist from Kelechi Iheanacho.
Both teams created good chances but failed to score in the first half.
Sadiq Umar missed what should have been the game's first goal in the 24th minute.
In the 15th minute, Semi Ajayi also missed a goal by nodding above the goalpost.
Guinea Bissau is eyeing its last hope as they lock horns with already qualified and top-of-the-group Nigeria.
Although they came to the tournament with many absences and technical changes, Nigeria's Super Eagles established themselves as one of the favourites with an outstanding performance in their first two matches.
A convincing victory over Egypt, followed by another against Sudan, ensured the Super Eagles qualified at the group's top, regardless of the outcome of Wednesday's match.
This is the first encounter between Guinea-Bissau and Nigeria at the Africa Cup of Nations.
Guinea-Bissau remains winless in their eight matches in the Africa Cup of Nations (D3 L5).
Nigeria has won 11 of their last 13 Africa Cup of Nations matches (L2), including both in this year's tournament. They last won their opening three games of an edition in 2006.
Guinea-Bissau is yet to score in this year's Africa Cup of Nations despite attempting 16 shots with an xG total of 2.21 in their two matches. Overall, they have failed to score in their last six Africa Cup of Nations matches; no nation has ever gone seven straight games without a goal in the competition's history.
If Nigeria wins, they will be the only team that qualified for the last 16 rounds, winning all group matches at the 33rd AFCON.