Christian Obodo and substitute John Obi Mikel struck in the second-half to give the Super Eagles victory in a slow paced encounter.
Nigeria are in charge of their Group D on 6 points, three points ahead of Senegal and Ghana who share second place.
Zimbabwe virtually lost their chance of qualifying to the second round after failing to bag any points in their first two matches.
Both sides got of to a slow start and gave a below-par display in the first-half.
Nigeria coach Augustine Eguavoen injected some life into his side by fielding Mikel and Nwankwo Kanu after the break.
Kanu nearly mad an impact on his first touch when he was brought down in the area, but his penalty claim was waved off.
Eguavoen’s substitutions finally paid off in the 57th minute Obodo connected with a Mikel corner-kick to head home the opener for Nigeria.
Mikel added the second when unleashed a powerful drive from the edge of the area to beat Gift Muzadzi one minute past the hour.
Nigeria conclude their group stage matches against Senegal on Tuesday while Zimbabwe take on Ghana.