Only about 200 masked people were allowed to attend Saturday’s service, which marks the period between Christ’s crucifixion and his resurrection on Easter Sunday.
For the second year in a row, the Vatican cut out the traditional sacrament of baptism for a handful of adults.
This year’s vigil service also started earlier than usual to respect Italy’s 10:00 pm COVID-19 curfew.
The service began with the pope lighting a single candle in the darkened Basilica and then sharing its flame with others until the pews slowly begin to twinkle and the Basilica's lights are turned on.
In his homily, Pope Francis said Easter offers a message of hope and new beginnings.
“In these dark months of the pandemic, let us listen to the risen Lord as he invites us to begin anew and never lose hope,” he said.
“It is always possible to begin anew, because there is a new life that God can awaken in us in spite of all our failures.”
Pope Francis limped considerably through the service, in a sign that the 84-year-old Argentine is suffering through a prolonged bout of sciatica nerve pain.
On Sunday, Pope Francis presided over Easter Mass before a similarly small group and delivered his traditional “Urbi et Orbi” (to the city and the world) blessing.
The pontiff focused his message on the world’s most vulnerable – the sick, migrants, people facing economic hardship, and those living in war zones like Syria, Yemen and Libya.
He also pushed for a more effective and rapid rollout of the COVID-19 vaccine.
“Vaccines are an essential tool in this fight,” he said, calling on the international community to overcome delays in distributing vaccines, “especially in the poorest countries”.
Usually the Easter Mass and blessing is celebrated before tens of thousands of people in St Peter’s Square.