Keshi's men fought hard but were beaten 2-0 by France in Brasilia, ending their campaign at the round of 16.
Afterwards, the 52-year-old, who took over in 2011 and led Nigeria to Africa Cup of Nations glory last year, announced he would be stepping down.
"Friends, it has been a good run and I have enjoyed every moment. It's been an honor (sic) coaching the Super Eagles. It is however time to bow out," Keshi tweeted from his official account.
The federation's official account retweeted a story posted by FIFA which said Keshi announced he was stepping down.
Keshi quit Nigeria after their Cup of Nations win last year, only to reverse his decision the following day.
Nigeria captain Joseph Yobo has also represented his country for the last time, announcing his international retirement after earning 100 caps.
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