The East African nation came into the match aiming at getting morale-boosting win after a 0-0 draw against minnows Turkmenistan in the previous game.
For Ivory Coast things were a bit different after a 3-1 win against Comoros, and another win could have ensured the team go into the Africa Cup of Nations finals with their heads high.
It was a perfect opportunity for each tactician to test their probable XI ahead of the continental finals, which kick off on June 21 in Egypt.
Farouk Miya scored the only goal in the 35th minute from the penalty spot to hand his team a narrow win.
Despite the introduction of Wilfred Bony and his namesake Zaha, Uganda managed to hold on and claim a historic win ahead of the tournament.
Uganda will open their Afcon campaign against DR Congo on June 22 in Cairo, while Ivory Coast face South Africa two days later in their opener.