The move comes barely two weeks after the NFF opened an investigation into reports that Keshi applied to manage Ivory Coast while under a valid contract with Nigeria.
Keshi recently claimed an un-named agent had submitted his name without his knowledge for the Ivory Coast position.
the Nigeria Football Federation has decided to exercise its option to summarily terminate the employment contract of Mr. Stephen Keshi with the Federation with immediate effect
An NFF statement outlined his fate.
"Having thoroughly reviewed the reports/findings of the NFF Disciplinary Committee and NFF Technical and Development Committee, as well as having reviewed the actions and inactions of Mr. Stephen Keshi, in the performance of his duties as Super Eagles' Head Coach, which we found to lack the required commitment to achieve the Federation's objectives as set out in the Coach's employment contract."
"To this end and pursuant to the provisions of Clause 4.3 of the Employment Contract between Mr. Stephen Keshi and the NFF (The Contract) and the various clauses therein, the Nigeria Football Federation has decided to exercise its option to summarily terminate the employment contract of Mr. Stephen Keshi with the Federation with immediate effect."
The NFF also said Keshi's sacking was "without prejudice to the settlement of any existing and due financial obligations between the NFF and Mr. Keshi."
Keshi, a former captain of the national team, led the side to the 2013 Nations Cup title in South Africa and also qualified the Super Eagles for the 2014 World Cup in Brazil, where they reached the second round before losing to France.
His contract was not renewed after the World Cup but he later returned on a match-by-match deal, which ended in November after failure to reach the 2015 Nations Cup.
As caretaker coach, Keshi endured a turbulent 2014, in which he was sacked by the NFF and only reinstalled after intervention from then Nigeria President Goodluck Jonathan.
The 53-year-old, who returned for his third spell in April, led his side to a 2-0 home win against Chad in a 2017 Africa Cup of Nations qualifier in June, but has now been shown the exit door after less than three months in charge.
Meanwhile, Shaibu Amodu who was formally appointed the country's technical director last week, takes over as caretaker coach and will be assisted by Salisu Yusuf until a permanent successor is appointed.
Amodu who has previously managed the national team on four different occasions returns to the helm for a fifth time.
He led Nigeria to a third-place finish in the 2002 Nations Cup and also held the job between 1994 and 1997.
Amodu previously helped the country to qualify for the 2002 World Cup in Japan and South Korea.
Under his stewardship, Nigeria qualified for the 2010 World Cup in South Africa but Amodu was sacked despite the team's third-place finish at the 2010 Africa Cup of Nations in Angola.
It was the second time he had been removed from his post ahead of a World Cup finals tournament - Amodu was also fired ahead of the 2002 edition after Nigeria finished third at the 2002 Nations Cup in Mali.
Stephen Keshi has been sacked as coach of Nigeria and replaced by Shaibu Amodu, the country's Football Federation (NFF) has announced.