It is unclear from MSF's statement the condition of the third patient. But the group said its ambulance staff were also assaulted in the incident by "law enforcement officers and members of a self-defence group".
MSF said staff were "violently attacked, insulted, tear-gassed, threatened with death" and held hostage for more than four hours before being released. The motive behind the attack is unclear.
"The act is a shocking display of violence and it seriously calls into question MSF's ability to continue delivering essential care to the Haitian people," said Christophe Garnier, the group's head of mission in the country.
MSF, also known as Doctors Without Borders, is one of the last humanitarian non-government organisations (NGOs) still operating in Haiti, where violent chaos has gripped the capital.
Since the assassination of President Jovenel Moïse in 2021, armed gangs have seized power in many areas, leading to a spike in street violence in the poorest country in the Americas.
A UN Security Council briefing last month heard that criminal gangs had gained control of 85% of the capital.
More than 3,600 people have been killed in Haiti since January and more than 500,000 have had to leave their homes, according to the UN.
The UN has sent an international policing operation to Haiti, largely made up of Kenyan police. The mission is said to have secured some key sites in the capital including the national hospital, seaport and airport.
However, several US airlines suspended flights to the country this week after three planes were hit by gunfire approaching or departing the airport this week.
A new prime minister was sworn into office in Haiti earlier this week. Alix Didier Fils-Aimé said his priority was "restoring security" in the country.
