Violet Nanjala lost a last minute spot kick in the first leg at Nyayo while Cynthia Shilwatso couldn't find the target from the spot in the return leg.
Harambee Starlets will miss the 2024 Africa Women's Cup of Nations finals after losing 2-1 to Botswana on aggregate in the final round of the qualifiers.
Starlets fell 1-0 to Botswana in the return leg played on Tuesday at the National Stadium to bow out of the contention for a place in the finals on the barest of margins.
The Kenyan girls had played Botswana to a one-all draw in the first leg held at the Nyayo National Stadium a week ago leaving them with an heavier task of winning away.
That did not happen as Botswana capitalized on home advantage to win by a solitary goal scored by Keitumetse Dithembe in the second half.
Dithembe was also on target in the first leg.
Starlets will have themselves to blame for wasting two penalties which would have gotten them over the line at the expense of Botswana.
Violet Nanjala lost a last minute spot kick in the first leg at Nyayo while Cynthia Shilwatso couldn't find the target from the spot in the return leg.
Botswana goalkeeper Maitumelo Bosija who is attached to African champions Mamelodi Sundowns saved both penalties.
Starlets had eliminated Cameroon in the previous round on post-match penalties after playing for a 1-1 result in both legs.
Had Kenya beaten Botswana on aggregate, they would have sealed return to the continental tournament after seven years in the cold.
Botswana who reached the quarter finals of the tournament in the previous tournament will be making their second appearance following their qualification.