Both goals came from set-pieces as Patrick Kaddu headed home a 14th-minute corner and then Emmanuel Okwi got a touch onto a free kick just after halftime.
Uganda last won at the finals in 1978 when they beat Nigeria in the semi-finals and finished runners-up to hosts Ghana.
Saturday’s surprise win served notice of the potential of a team not given much chance of progressing past the first round.
Kaddu attacked the ball at the near post and got a sharp angle to his twisting header for the first goal.
He had a good chance to score a second, also with a header from a cross-field ball, just three minutes later but put it wide of the target as the Congolese defence was beaten again.
Uganda also shaved the crossbar with a shot from Farouk Miya four minutes from halftime while at the other end their goalkeeper Denis Onyango had his first save after 43 minutes when he stopped Cedric Bakambu’s effort.
Okwi’s goal came when he looped the ball over Congolese goalkeeper Ley Matampi with a flick-on.
Miya almost made it 3-0 in the 56th minute with a rasping shot that Matampi did well to save while Congolese substitute Jonathan Bolingi hit the Uganda crossbar with a 70th-minute header.
The result is a setback for the languid-looking Congolese, who were semi-finalists in 2015 and quarter-finalists two years ago.
The match was played in soaring temperatures of over 30 degrees Celsius and in front of a largely empty stadium, in stark contrast to Friday’s opening game where some 70,000 fans packed into the iconic venue for the opening game of the tournament as hosts Egypt beat Zimbabwe 1-0.
(Reporting by Mark Gleeson; editing by Tony Lawrence)
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