Doctors had to put him on non-invasive mechanical ventilation following a coughing fit in which he inhaled vomit that needed to then be extracted.
Doctors said it would take a day or two to evaluate how and if the episode affected Francis' overall clinical condition.
His prognosis remained guarded, meaning he was not out of danger.
"The night has passed quietly, the Pope is resting," the Vatican said in a brief morning update on Saturday.
In the late Friday update, the Vatican said the 88-year-old suffered an "isolated crisis of bronchial spasm", a coughing fit in which Francis inhaled vomit, that resulted in a "sudden worsening of the respiratory picture".
Doctors aspirated the vomit and placed Francis on non-invasive mechanical ventilation.
The Pope remained conscious and alert at all times and cooperated with the manoeuvres to help him recover.
He responded well, with a good level of oxygen exchange and was continuing to wear a mask to receive supplemental oxygen, the Vatican said.
The episode, which occurred in the early afternoon, marked a setback in what had been two successive days of increasingly upbeat reports from doctors treating Francis at Rome's Gemelli hospital since February 14.
The Pope, who had part of one lung removed as a young man, has lung disease and was admitted after a bout of bronchitis worsened and turned into pneumonia in both lungs.
The Vatican said the episode was different to the prolonged respiratory crisis on February 22, in that it was an isolated spasm that resulted in Francis aspirating the vomit that he produced.
Doctors did not resume referring to Francis being in "critical condition", which has been absent from their statements for three days.
But they say he is not out of danger, given the complexity of his case.
Late on Friday, Francis' closest friend in the Vatican bureaucracy, Argentine Cardinal Victor Manuel Fernandez, led the nightly prayer in St Peter's Square to pray for Francis' health.
With other cardinals bundled against the night chill, Fernandez urged the crowd to pray not just for Francis but for others, as the pope himself would.
"Certainly it is close to the Holy Father's heart that our prayer is not only for him, but also for all those who in this particular dramatic and suffering moment of the world bear the hard burden of war, of sickness, of poverty," said Fernandez, the Vatican's doctrine chief.
Also on Friday, the Vatican published a document signed by Francis on February 26 "From the Gemelli Polyclinic", a new official tagline that showed Francis was still working from the hospital.
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