During the siege of Petersburg, he commanded the 2nd Brigade, 1st Division, X Corps at Chaffin's Farm and the subsequent actions along the Darbytown and New Market Roads. The Army of the James was then reorganized and his command became the 2nd Brigade, 2nd Division, XXIV Corps which was attached to the Fort Fisher Expeditionary Corps under Brig. Gen. Alfred H. Terry and participated in the second battle of Fort Fisher and the capture of Wilmington. Although Abbott was not appointed as a full, substantive rank general, on January 25, 1865, President Abraham Lincoln nominated Abbott for appointment to the grade of brevet brigadier general of volunteers, to rank from January 15, 1865 for gallant services in the capture of Fort Fisher and the U.S. Senate confirmed the award on February 14, 1865. During the final stages of the war, he was stationed in Wilmington, North Carolina.