The veteran forward headed home from a free-kick just before the break as his side held on to claim the vital victory and book their place at the knockout stage.
Uganda have themselves to blame for finishing a game they dominated empty, a result which keeps their chances of progressing out of the group hanging by the slimmest of margins.
It was the experience of Zambia, who had in their team Africa Cup of Nation winners’ Katongo and Isaac Chansa that made the difference.
Early in the game Katongo was unlucky to put his side in front with a chip past Uganda goalie Mathias Kigonya only for Denis Okot to clear the ball off the line.
The Cranes had some good moments to break the deadlock but failed to do so and Zambia punished them on 41 minutes, when Katongo soared above his marker to head home for what turned out to be the only goal of the match.
The second half was equally enterprising with Uganda pressing more in search of the equalizer. Dennis Awany failed to connect Robert Sentongo’s assist whilst Kizito Keziron shot wide with Zambia goalie Jacob Banda at his mercy minutes later.
Uganda survived a late Zambia scare after Clatous Chama profited from a counter attack, rounded Kigonya only for a defender to weather the storm with a timely clearance.
Zambia will next play Mali in Kigali whilst Zimbabwe squares Uganda in Rubavu both on Thursday.
Orange Man of the Match
Christopher Katongo (Zambia)