Jones was sent to the Richmond area afterwards to serve under Maj. Gen John B. Magruder's command, and he was promoted to major general on March 10, 1862.

Jones became the highest ranking division commander in the Army of Northern Virginia after Maj. Gen Richard Ewell was wounded at Groveton on August 28.

At Antietam, his division held the right flank of the Army of Northern Virginia when the Union IX Corps attacked across the Burnside Bridge.

He was quickly re-appointed as a major general on October 10, but it now meant Jones was junior to several other division commanders in the Army of Northern Virginia, including John Hood and George Pickett.

Kingsbury, at Antietam, coupled with the strain of campaigning aggravated a longstanding heart condition, led to Jones being unable to command due to his health.