The 80-year-old pope lay for several minutes before the central altar. He wore crimson-colored vestments for the day commemorating the crucifixion of Jesus.
Several times during the service, Francis bowed his head in silent reflection.
Papal preacher the Rev Raniero Cantalamessa told the faithful they were recalling the "violent death" of Jesus 2,000 years ago, even when most days bring news of violent deaths, because his crucifixion "changed forever the very face of death."
Cantalamessa called the cross the definitive "'No' of God to violence, injustice, hate, lies."