Sunday Chidzambwa's side were on level terms in Cairo at the time of the miss after Khama Billiat cancelled out Emmanuel Okwi's opener.
But Zimbabwe, beaten 1-0 by host Egypt in its opening match last week, missed its big opportunity to get a first win in this year's competition as captain Musona somehow missed an open goal from four yards.
Uganda held on for a draw to add to the three points collected against DR Congo - its first AFCON win in 41 years.
Uganda had won two of its previous 15 meetings with Zimbabwe in all competitions, but it was in front inside 12 minutes as Lumala Abdu's shot was parried by back-up keeper George Chigova and Okwi had a simple close-range finish.
That goal sparked a response from Chidzambwa's men, with Musona lifting a shot over the bar from eight yards and Billiat dragging a shot wide.
Billiat made amends for that miss five minutes before half-time, though, as he rounded off a fine team move by getting in front of his man to divert Ovidy Karuru's cross away from goalkeeper Denis Onyango.
Then came Musona's incredible miss six minutes into the second half - the Anderlecht-owned striker only managing to pick out the crossbar despite having a completely unguarded net to aim for when the ball dropped into his path in front of goal.
Billiat had a first-time shot kept out by Onyango and Patrick Kaddu volleyed over a glorious opportunity late on at the other end as the spoils were shared.