Nigeria defender Godfrey Oboabona struck home an 83rd-minute free-kick to deny Namibia an upset after the plucky hosts had gone ahead through substitute Deon Hotto in the 77th minute.
Nigeria stay top of Group F, two points ahead of Malawi, who drew 2-2 with Kenya earlier on Wednesday, going into the last round of matches in September.
The result continued Nigeria's patchy form since winning the African Nations Cup finals in February and will have come as a blow to morale ahead of their participation in the Confederations Cup in Brazil, which starts on Saturday.
A win for Nigeria on the artificial surface of the Sam Nujoma Stadium would have ensured top spot in the group and a place in October and November's final round of play-offs for the 2014 finals.
They must now wait until September when they host Malawi, needing at least a draw to progress.
After dominating from the start and coming close on several occasions in the first half, Nigeria let the game slip in the second and looked relieved at the end with their share of the spoils.
Nigeria's Ahmed Musa, their best player on the night, proved a livewire attacker and some superb saves from Namibia's goalkeeper Virgil Vries stopped the Super Eagles from running away with the match.
Nigeria might have gone ahead after 40 seconds when Vries made a double save to deny Nnamdi Oduamadi and Anthony Ujah.
Soon after John Obi Mikel, who drifted in and out of the game, went narrowly wide with a free-kick.
Musa's persistence down the wing opened up more opportunities and a clever backheel by the Russian-based player set up Ujah, who shot straight at the goalkeeper.
Musa's pace carved out a similar chance on the stroke of half-time only for Vries to block the opportunity on the stretch.
Oduamadi beat the offside trap to find himself clear at the back post in the 66th minute but seemed surprised when the ball reached him and put his header into the side netting.
A swift counter attack and some smart passing then allowed Hotto to score from close range to the delight of the partisan crowd.
Namibia, however, gave away an unnecessary free-kick seven minutes from time and paid a heavy price.