Ameobi preferred to skipper a depleted Magpies team that slumped 2-0 at second-tier Brighton and Hove Albion on Saturday to make a shock FA Cup third-round exit.
The 31-year-old striker made his senior international debut against Venezuela two months ago and was set to be included in a 23-man Super Eagles squad for the Cup of Nations between January 19 and February 10.
But once Ameobi was chosen in a provisional Nigerian squad, Newcastle manager Alan Pardew said the player would not be going to South Africa for the tournament without giving a reason.
Although it emerged that a clause in the contract of Ameobi allowed the English Premier League club to retain his services during the tournament, Eagles coach Stephen Keshi did not drop him from the squad until this weekend.
“The chapter concerning Ameobi is now closed and we are looking ahead to the announcement of the final 23-man squad this week,” Nigeria team spokesman Ben Alaiya told reporters at the camp in Faro.
Alaiya added that the final squad list could be named Tuesday, a day before Nigeria play a warm-up match against the Cape Verde Islands in Portugal.