At the battle of Chancellorsville (1-4 May 1863), Lee commanded the only full brigade of cavalry operating with the main army, Stuart having been detached to counter a move by the Union cavalry. Lee's troopers uncovered the fact that the Federal right flank was unprotected and vulnerable to attack. This led to "Stonewall" Jackson's famous flanking march, which Lee's cavalry ably screened. That summer, he was with Stuart again for another ride around the Union army during the Gettysburg campaign, a maneuver that effectively removed the Confederate cavalry from meaningful participation in the campaign and kept them off the Gettysburg battlefield until the third day of fighting. On that day, 3 July 1863, Lee took part in the major clash in which Stuart's forces were bested by the Union cavalry. On 3 August 1863 Lee was promoted to major general, and the following month he was given command of a division of cavalry, which he led under Stuart's overall command until the latter's death in May 1864.
Steven E. Woodworth, "Lee, Fitzhugh," American National Biography Online, February 2000, http://www.anb.org/articles/05/05-00428.html.