The global football governing body was poised to suspend Nigeria from world football - a move also affecting club teams, referees and officials - when a peace agreement was reached on Monday.
However, Fifa spokesperson Nicolas Maingot says it will "continue to monitor the situation closely".
The dispute began when Nigerian President Goodluck Jonathan banned the national teams and ordered a probe into alleged corruption at the football federation after the Super Eagles' early World Cup exit.
Jonathan's decree breached Fifa rules, which forbid governments from intervening in football's affairs.
Jonathan said on Tuesday that hundreds of posts on his Facebook page had helped persuade him to reverse his suspension of the national soccer team from international competitions.
"To Suleiman Musa, Nwanze Francis Uchenna and Ifade Udunayo Peter and the hundreds of Nigerians who appealed to me on this page, I have listened to your voices and those of others," Jonathan said.
"We must now work together to make sure the Nigerian Football Federation and our players do us proud in future events," he wrote on the networking site.