Orthodox believers were asked not to take part in Roman Catholic services and a Church delegation due to attend also stayed away.
But Church officials said the decision had been taken by mutual agreement.
It was one of the smallest crowds seen at an outdoor papal Mass during Francis's foreign trips.
People who did attend in the capital Tbilisi said afterwards that the papal visit was good for Georgia.
"This is a very significant event, both for the country and for faithful from the whole Catholic parish," Keti Khitarikhvili told Reuters news agency.