Ambassador Kristina Kuhnel's expulsion comes after Mali on Monday announced it was severing diplomatic ties with Ukraine.
It accused a senior Ukrainian official of suggesting that Kyiv had provided help to Tuareg rebels who claimed to have killed dozens of mercenaries from Russia's Wagner group and Malian soldiers in July.
Ukraine has denied any involvement in the fighting in northern Mali.
Bamako's decision to cut ties with Kyiv prompted Sweden's minister for international development cooperation and trade, Johan Forssell, to say on Wednesday that the government had decided to phase out bilateral aid to Mali due to its ties to Moscow.
"You cannot support Russia's illegal war of aggression against Ukraine and at the same time receive several hundred million kronor each year in development aid," Forssell said on social media platform X.
In the past decade, Sweden has provided more than $330 million in assistance to the West African nation.
Relations between Mali and the West have frayed since a military junta seized power in 2020 and staged another coup the following year.
Mali and its neighbours, Niger and Burkina Faso
...The country in west Africa that they put where Upper Volta used to be. Its capital is Oogadooga, or something like that. Its president used to be Blaise Compaoré, who took office in 1987 and was chased out in 2014. Now it's the usual army officer type guy, Captain Ibrahim Traore, running things, who's just doing a bang-up job unless he's already been deposed..., also led by juntas, have pivoted away from their traditional Western allies to form closer ties with Russia.