Kenyan police fired tear gas to disperse protesting spectators after a stunning 1-0 home defeat by minnows Guinea-Bissau Sunday in a 2017 Africa Cup of Nations qualifier.
Trouble erupted at the Nyayo National Stadium in Nairobi when the visitors snatched a late lead through a disputed Sanchez Semedo goal.
Harambee Stars players and supporters believed the ball did not cross the line and TV replays were inconclusive.
Play was temporarily halted by the Zimbabwean referee and Kenya are set to be punished by the African Football Confederation (CAF).
Victory completed a double over Kenya for traditional whipping boys Guinea-Bissau, ranked 18 places lower in Africa, after a home 1-0 win four days ago.
Gaining maximum points lifted the team from the Portuguese-speaking West African country to the top of Group E, one point ahead of co-favourites Congo and Zambia, who drew 1-1 in Brazzaville.
The match produced the same result and the same scorers as the first meeting in Zambia last Wednesday.
Both goals came after goalmouth scrambles with Jordan Massengo giving Congo an early second-half lead and Winston Kalengo equalising.
Zambia almost won at the death with a Christopher Katongo shot deflected on to the roof of the net.
Guinea-Bissau have seven points with two qualifying rounds to come in June and September, Congo and Zambia six each and Kenya one.
All group winners are guaranteed places at the 2017 tournament in Gabon, but just the best two of 11 runners-up in the four-team groups join them.
The withdrawal of cash-strapped Chad Sunday after three consecutive defeats has reduced Group G to three teams, meaning only one from Egypt, Nigeria and Tanzania can make it.
Egypt have four points, Nigeria two and Tanzania one in the revised standings ahead of a Tuesday clash between the Pharaohs and Super Eagles in Alexandria.
Should record seven-time African champions Egypt win, Nigeria will be eliminated and miss the finals for the third time in four editions.
Ghana, runners-up to Ivory Coast in the last Cup of Nations, surrendered a perfect 2017 qualifying record when held 0-0 by Mozambique in Maputo.
A sleep-inducing affair produced hardly any clearcut chances with both teams showing the effects of having to play twice in four days.
Botswana avenged a midweek Group D loss in the Comoros by winning 2-1 in Francistown and Benin went top of Group C by trouncing South Sudan 4-1 in Cotonou.