The 34-year-old was seven months pregnant when she died and had been working as a secretary at guest house Santa Marta for the last four years.
It has been reported by The New York Post that she suffered from a severe form of diabetes and that doctors had suggested pregnancy posed a risk.
Pope Francis laid long-stemmed white roses at Miriam Wuolou's memorial in the church of Santo Stefano degli Abissini.
He then blessed the site and paid his respects.
The Director of the Holy See Press Office, Fr Federico Lombardi, said before the funeral Mass that Pope Francis prayed silently "showing his great affection and respect for his dear collaborator in the Casa Santa Marta."
Pope Francis has recently returned from a trip to Mexico.
Police are investigating Miriam's death and looking into the possibility that neglect could have contributed to her death.
Her body was found in her apartment in Rome by police, after her brother had voiced concern that she had not been answering her phone.
It has been reported that police have interviewed her brother, her ex-husband and most recent boyfriend, according to the Italian newspaper Il Messaggero.
The investigation continues.
