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.
"He is a true pope, he is not just a religious figure, but also a very political figure. Because I think that with this visit, the role of Georgia will be raised measurably on the world stage."
With a Roman Catholic population of under 1%, it was not an obvious destination but the Pope has made a point of reaching out to Orthodox churches to overcome doctrinal differences which split the two communities in the 11th Century.
The late Pope John Paul II visited Georgia in 1999, and he was treated as the Vatican head of state, rather than a religious leader.
Georgia, a small country (population 4.3 million) in the Caucasus Mountains, shares an Orthodox culture with the regional superpower, Russia, but the two fought a brief war in 2008.
Vatican attempts to mend ties with the Russian Church have so far not resulted in a papal visit there. On the other hand, Georgia aspires to join the EU and Nato.
Why the boycott?
According to the Associated Press, only a few thousand people attended the Mass in the Meshki stadium, which has a capacity of 25,000.
The Orthodox patriarchate said on its website: "As long as there are dogmatic differences between our churches, Orthodox believers will not participate in their prayers".
One Georgian priest told AP it was a protest against Catholic attempts to convert Orthodox Christians.
"Can you imagine how it would be if a Sunni [Muslim] preacher came to Shia [Muslim] Iran and conducted prayers in a stadium or somewhere else?" Father David Klividze asked. "Such a thing could not be."
Nonetheless, the Church leader, Patriarch Ilia, had welcomed Pope Francis on Friday as his "dear brother" and toasted him saying "May the Lord bless the Catholic Church of Rome".
Georgian President Georgy Margvelashvili did attend the Mass. Other politicians may have stayed away because of forthcoming elections, for fear of upsetting devout voters.
On Sunday, the Pope is due to visit neighbouring Azerbaijan, which has fewer than 300 Catholics in its overwhelmingly Muslim population.
However, religious coexistence is a major theme for Pope Francis who visited Muslim-majority Turkey in November 2014.