Andre Ayew struck from 12 yards to give Ghana a winning start to their AFCON campaign in Gabon.
The West Ham forward made no mistake from the spot in the 32nd minute after Asamoah Gyan was brought down in the penalty area.
In a nervy second half the Black Stars were unable to add to their lead but held on to claim a vital three points over Uganda.
The result also means Ghana have now won four of their 11 matches against Uganda.
Avram Grant, a former Chelsea manager, is looking to lead Ghana to a second successive final but go better than 2015 when his team lost to Ivory Coast.
Uganda have also finished runners-up in the continental championship but the trip to the final in 1978 was also the last time they qualified until making the Gabon event.
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