The 83-year-old pontiff, who lost part of his lung to a respiratory illness as a young man, paused twice while addressing pilgrims on Sunday.
At the end, he asked for prayers for the Lenten retreat, adding "unfortunately a cold prevents me from participating this year... I will be following the meditation from here".
The Vatican described Francis' condition as "a slight illness" without giving further details.
It comes amid general alarm in Italy over the coronavirus outbreak, which has infected more than 1,100 people, mostly in northern Italy.
The pope's weekly appearance from a window high above St Peter's Square was the first time he had been seen publicly since Ash Wednesday, when he was coughing and blowing his nose during mass.
The pope has cancelled several official engagements this week - including two planned official audiences - over the illness.
He was due to leave on Sunday for the retreat in the Roman countryside.
Such retreats for members of the Society of Jesus - a religious order to which he belongs - are typical.
