Francis Kimanzi suffered his first defeat as Kenyan coach after falling by a solitary goal against Mozambique in a friendly played on Sunday.
A second-half strike by Canhembe Amancio was enough to give the visitors their first win in four attempts against the Harambee Stars and deny the Kenyans a chance to shine at home.
The defeat came a day after Kenyan marathon runner Eliud Kipchoge made distance running history in Vienna on Saturday.
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Kipchoge became the first man to run the marathon in under two hours after clocking one hour, 59 minutes and 40 seconds during the INEOS 1:59 Challenge at Prater Park in Austria.