In the 83rd minute of the clash and with the score tied at 1-1, Alex Iwobi threaded an incisive pass through for Musa, who also had substitute Isaac Success chasing it.
The Al Nassr forward opted to have a go instead and slotted past Itumeleng Khune to put the Super Eagles ahead, but referee Bakary Gassama ruled it out for an offside.
Replays, however, showed the referee and his assistant got the call wrong as both players were few metres behind a Bafana Bafana defender.
Earlier in the first half, Musa was involved in a similar incident and was unlucky not to register an assist with strike partner Kelechi Iheanacho's tap-in ruled out for offside.
Eventually, those would matter less as a draw was enough for Gernot Rohr's men to make a return to the continental showpiece, with a game to spare.
However, amid several celebratory tweets and Instagram posts from players of the team, the captain took to his Twitter to question the decision, calling out Caf in the same post.
The rejuvenated forward will hope to get lucky if picked by Rohr for Tuesday's friendly against Uganda at the Stephen Keshi Stadium, Asaba.