Yasuyoshi Chiba, a 42-year-old Japanese national, was hospitalised in a Rio clinic after bleeding profusely from the head. He received three stitches and underwent computer tomography that determined that he was in satisfactory condition.
The incident occurred during a clash between rioters and police near the Rio state government headquarters where Pope Francis earlier met with President Dilma Rousseff shortly after he started a week-long visit to Brazil.
"I saw a demonstrator fall to the ground. Police grabbed him and took him away," Chiba said. "I took pictures of the scene, and was suddenly pushed by other police officers.
"I then raised my hands with my camera to show that I was a photographer. That is when a uniformed policeman with a shield hit me with his truncheon on the head."
Chiba, who began his career in Japan, later worked for AFP in East Africa before he was assigned to Brazil two years ago, first in the Sao Paulo office and now in Rio.
Earlier in the city, riot police used tear gas, water cannon and stun grenades to disperse scores of rioters who hurled firebombs.
The violence, which led to five arrests, followed a tense standoff between police and hundreds of Anonymous "hacktivists" and gay militants rallying against Rio state Governor Sergio Cabral's policies as well as against $53m spent on the Argentine-born pope's landmark visit.
The first Latin American pope is here to meet with young pilgrims from around the world attending World Youth Day, a major Catholic festival.