The win placed the East Africans level on points with hosts Egypt who beat Zimbabwe 1-0 on Friday in the opening match, but they are ahead on goal difference.
Patrick Kaddu opened scoring for the Cranes with a header from a corner kick, following a well-timed run to the near post after just 14 minutes.
Kaddu’s strike partner Emmanuel Okwi doubled the lead for Uganda with a glancing header in the 48th minute.
Substitute Jonathan Bolingi had the best opportunity for DR Congo but the Belgium-based forward’s header struck the top of the crossbar.
The News Agency if Nigeria (NAN) reports that Uganda will go on to face Zimbabwe on Wednesday in their next match, with DR Congo taking on Egypt later that day.