In a declaration by summit participants, the importance of promoting women's rights was stressed repeatedly.
The U.S. embassy in Kabul, condemning the public execution in the "strongest possible terms", said the hard-won gains of Afghan women made in the last 10 years must be protected.
But Shah Jahan Yazdanparast, head of women's affairs in Parwan, which is connected to the Kabul ministry, said such naked violence as the woman's execution "will only increase our fear and concern as women in Afghanistan".
Afghan women have won back basic rights in education, voting and work since the Taliban were ousted from power but fears are mounting both at home and abroad that such freedoms could be traded away as Kabul seeks peace talks with the group.
"Afghan women and girls were looking to the international community to protect the progress they have made in the last decade and they have been let down," Oxfam Afghanistan's head of policy and advocacy, Louise Hancock, said on Sunday after the close of the Tokyo summit.
Violence against women has increased sharply in the past year, according to Afghanistan's independent human rights commission. Activists say there is waning interest in women's rights on the part of President Hamid Karzai's government.
Authorities blamed the Taliban for the stoning to death of a young couple in northern Kunduz province two years ago in a crowded bazaar, days after a pregnant widow was flogged and killed in western Baghdis province. The Taliban denied involvement.
(Additional reporting and writing by Amie Ferris-Rotman; Editing by Robin Pomeroy)