Nineteen-year-old Sylvester Bonnaffon Jr. enrolled for military service in Philadelphia, Pennsylvania on December 14, 1861, and mustered in there that same day as a private with Company I of the 99th Pennsylvania Volunteer Infantry. Transferring to Company G within the same regiment on December 18, he was then promoted to the rank of corporal on April 1, 1862 and to the rank of sergeant a month later (on May 1). Commissioned as a second lieutenant on August 1 of that same year, he subsequently engaged with his regiment in several of the most intense actions of the American Civil War as part of the Union's Army of the Potomac, including 1862's Second Battle of Bull Run (August 28–30) and battles of Chantilly (September 1) and Fredericksburg (December 11–15); 1863's Chancellorsville Campaign (April 30–May 6), battles of Gettysburg (July 1–3) and Wapping Heights (July 23), Bristoe Campaign and its First Battle of Auburn (October 13) and Second Battle of Rappahannock Station (November 7), and the Mine Run Campaign (November 27–December 2); and 1864's battles of the Wilderness (May 5–7), Spottsylvania Court House (May 8–21), North Anna (May 23–26), and Cold Harbor (May 31–June 12). Engaged with his regiment in the Siege of Petersburg, including the First and Second Battles of Deep Bottom (July 27–29, 1864 and August 14–20), he was then advanced in rank again with a commission to first lieutenant on September 27.