Felix Katongo scored Zambia's winner in Chililabombwe
Zambia took advantage of Togo captain Emmanuel Adebayor's absence to beat the group favourites 1-0 in their 2010 World Cup and Africa Cup of Nations qualifier.
Felix Katongo scored from 30 yards in Chililabombwe to put the Zambians top of Group 11.
Togo must now beat Swaziland in their final group game to have a realistic chance of qualification.
The 2006 World Cup finalists had a troubled build-up to the tie.
Adebayor refused to fly to Zambia on Tuesday after a row with the Togo Football Federation (TFF).
The Arsenal striker had demanded that TFF President Tata Avlessi Adaglo travel with them - a request which the TFF refused.
It followed coach Henri Stambouli's decision to quit last week.
The match had been rescheduled as a mark of respect for Zambian president Levy Mwanawasa, who died in August.
Zambia captain Christopher Katongo said that his team was mindful of Mwanawasa's death.
"The guys were mourning, we had two things in hand - it was a deciding game and we had lost our President," Katongo told BBC Sport.
"The second half wasn't as good as we had expected, but the important thing is we collected three points so that people can be happy in a sad moment."
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