Angola leapfrogged misfiring Uganda at the top of Group J when winning 2-0 in Guinea-Bissau to qualify for January's Africa Cup of Nations finals.
Manucho opened the scoring in the first half, before Mateus Galiano doubled the lead in the second period.
Uganda could have taken the ticket with a win at home to Kenya, but they were held to a 0-0 draw.
Angola qualified against the odds, winning their last two games while Uganda took just a point in that time.
The Palancas Negras finished the group with 12 points, one more than Uganda.
Kenya finished on eight points, with Guinea-Bissau bringing up the rear with just three.
Uganda had the best of the game in Kampala and really should have scored to claim the win they needed - but they were wasteful in front of goal and paid the price.
Coach Bobby Williamson told the BBC that he was devastated by their failure to qualify but said he hoped to complete his contract - which takes him up to the World Cup in 2014.
He acknowledged that the final decision on his position rested with the Ugandan Football Federation, Fufa.
Uganda had been hoping to reach their first Nations Cup since 1978, when they contested but lost the final.
Thousands of Ugandans who could not lay their hands on a ticket to the match packed clubs and restaurants to watch the game, but were seen leaving the venues crestfallen after the final whistle.
"It is a big disappointment that we did not score," said Fufa Head of Media Rogers Mulindwa.
"What has not been disappointing however is that the Cranes played relatively well and put pressure on the Harambee Stars."