Uganda secured their first goal in the 14th minute through a header by Kampala Capital City Authority (KCCA) striker Patrick Kaddu who converted a corner.
Emmanuel Okwi doubled the lead in the 48th minute with a glancing header from a free kick taken by Farouk Miya.
The Congolese never recovered from the two-goal deficit. The win not only places Uganda on top of group A with the hosts Egypt in second place, but also gives the Cranes a vital psychological boost to try to get out of the group stages.
It was a sweet victory for the Cranes but also a historic one. This is largely because the Ugandan side were considered under-dogs but also because D.R Congo boasts more foreign-based stars. The win is also historic in the last 2017 Afcon in Garbon, the Uganda failed to win a single game. The last win at Afcon was recorded 41 years ago during the games held in Accra, Ghana in 1978.
The Cranes return to action on Wednesday against Zimbabwe who lost to Egypt in the opening game.