Fahad Bayo was the match winner as Uganda registered their first 2022 Fifa World Cup qualifying goal and victory in Kigali last night.
The Cranes immediately ascended top of Group E on five points, a situation that was due a likely update from the late kickoff between Mali and Kenya.
This was the Cranes first victory over Rwanda on the Amavubi Stars home soil in 11 attempts.
It is also the first time Uganda are winning a competitive game since the 1-0 victory over South Sudan in the Afcon qualifiers last November.
The three points ahead of the return leg in Kitende on Sunday is the perfect gift for Uganda as the country celebrates her 59th Independence Day tomorrow.
Cranes coach Micho Sredojevic and his team's target of six points from this back-to-back affair remains firmly on track.
Only the group winner will advance to the playoffs due March 2022, from which five African representatives to the Qatar World Cup will be decided.
Micho started yet another World Cup qualifying game with a different goalkeeper, with Charles Lukwago returning after being benched for the draw against Mali.
Timothy Awany played his first game of the campaign alongside Enoch Walusimbi in central defence, while Taddeo Lwanga joined Captain Khalid Aucho, Bobosi Byaruhanga and Moses Waiswa in the midfield.
Steven Mukwala and scorer Bayo were tasked to tire the Rwandan defence whenever an opportunity arose.
Micho, who made all five of his substitutions in the second half including introducing Aziz Kayondo for injured Isaac Muleme, Cromwell Rwothmio, Yunus Sentamu and Martin Kizza, approached this rather cautiously.
The Rwandans had Uganda on the back foot for most of the first half, with Lukwago the busiest of the two goalkeepers.
Djabel Manishimwe, skipper Haruna Niyonzima, Kevin Muhire, Meddie Kagere and Rafael York all tested the Ugandan defence but the visitors held firm.
But as half time approached, and against the run of play, Rwanda conceded a free kick in a dangerous area.
Muleme drilled it in but the hosts failed to clear their lines.
The ball instead fell invitingly to Byaruhanga inside the penalty area, who drilled in a shot past goalkeeper Emery Mvuyekure and off the upright, with Bayo poking home the rebound on 41 minutes.
The Cranes did have one more good chance to bury the game midway the second half but Mukwala skied a free header from a brilliant delivery from the left.
Uganda, who defended for most of the second half, could have paid for that miss but Niyonzima miscued his effort with goal at his mercy.
The fight carries on to Sunday, when the Amabubi Stats try their lack here.
Qatar 2022 Fifa World Cup qualifiers
Group E fixtures and results
Match Day 1 results
Mali 1-0 Rwanda
Kenya 0-0 Uganda
Match Day 2 results
Rwanda 1-1 Kenya
Uganda 0-0 Mali
Match Day 3 results
Mali 5-0 Kenya
Rwanda 0-1 Uganda
Match Day 4, October 10
Kenya vs Mali
Uganda vs Rwanda
Match Day 5, November 11
Uganda vs Kenya
Mali vs Rwanda
Match Day 6, November 14
Mali vs Uganda
Kenya vs Rwanda
Play-offs, March 2022