Many of the players who beat Zambia to win the COSAFA Cup southern Africa title were in the team that beat Namibia 1-0 in Harare, but lost 5-4 on penalties.
Namibia converted all five spot-kicks, but Zimbabwe goalkeeper Herbert Rusawo had his saved to cost the "Warriors" the tie.
Prince Dube scored the only goal on 39 minutes at the National Sports Stadium, cancelling the first-leg advantage Namibia gained through a Hendrik Somaeb scorcher.
The exit of Zimbabwe after the second of three qualifying rounds for the
2018 Nations Championship in Kenya next January and February was a shock.
They had qualified for the four previous editions of a competition restricted to footballers registered with clubs in their country of birth.
With most African nationals squad composed almost exclusively of Europe-based players, the Nations Championship was introduced in 2008 to give local stars international exposure.
Matches have full international status, count toward the monthly FIFA rankings and caps are awarded.
Another factor that seemed to favour Zimbabwe was the rustiness of Namibia as there has been no domestic league football for more than a year due to feuding among officials.
Tiny island state Comoros booked a third-round tie against Namibia during August despite losing 1-0 to Lesotho at Setsoto Stadium in Maseru.
Reboame Koloti struck after only 12 minutes to get the home team off to an encouraging start, but they failed to score again and bowed out 2-1 on aggregate.
Madagascar upset Mozambique 2-0 in Maputo after being held at home with goals from Bela Claudel Fanomezana and Njiva Rakotoharimalala setting up a showdown against Angola.
Another unexpected second leg result was Liberia defeating Mauritania 1-0 in Nouakchott through a Christopher Jackson goal six minutes before half-time.
But the win was not enough to erase the damage caused by a 2-0 loss in Monrovia last weekend and Mauritania progressed to face Mali next month.
Benin squeezed past Togo 8-7 on penalties after another 1-1 draw between the west African neighbours, this time in Cotonou.
Warris Aboki gave Benin an early second half lead that Kodjio Sewonou cancelled with 18 minutes remaining.
22.07.2017 Kampala Uganda 5-1 South Sudan (0-0)
22.07.2017 Kigali Rwanda 0-0 Tanzania (1-1)
23.07.2017 Bujumbura Burundi 0-0 Sudan*
West Zone A
22.07.2017 Dakar Senegal 3-1 Sierra Leone (1-1)
22.07.2017 Bamako Mali 4-0 Guinea (0-0)
22.07.2017 Conakry Guinea 7-0 Guinea Bissau (3-1)
23.07.2017 Nouakchott Mauritania 0-1 Liberia (2-0)
West Zone B
23.07.2017 Cotonou Benin 1-1 (8-7pen) Togo (1-1)
22.07.2017 Moruleng South Africa 1-0 Botswana (2-0)
22.07.2017 Lusaka Zambia 3-0 Swaziland (4-0)
23.07.2017 Maseru Lesotho 1-0 Comoros (0-2)
23.07.2017 Maputo Mozambique 0-2 Madagascar (2-2)
23.07.2017 Luanda Angola 3-2 Mauritius (1-0)
23.07.2017 Harare Zimbabwe 1-0 (4-5pen) Namibia (0-1)