The "Battle of Bull Run" could apply to either of two battles, the First Battle of Bull Run (July 21, 1861) or the longer Second Battle of Bull Run (August 28-30, 1862). The former was called the First Manassas by the Confederates, who won the battle, and the latter Second Manassas, where the South also won, but not as conclusively.
At the First Battle, the Confederate forces were commanded by General P.T. Beauregard, who was under the overall command of General Joseph Johnston (whose troops arrived late in the battle).
At the Second Battle of Bull Run, the Confederate commander was Robert E. Lee, and he was able to force another Union retreat, only to be stopped in his campaign by the Battle of Antietam 19 days later.
It can be said with a degree of certainty, that the defeat of Pope's army at the Second Bull Run, led the way to Lee's invasion of Maryland, however, there were military operations on both sides prior to that invasion. It can also be said that if the above mentioned operations had been handled differently, the invasion of Maryland by the Army of Northern Virginia, might have been delayed, or prosecuted in another manner than which it was.
(see the related links below for the two battles)
Technically speaking, General Joseph E. Johnston was in command of the Confederate forces at the First Battle of Bull Run. He commanded the Army of the Shenandoah Valley, while General Pierre G.T. Beauregard commanded the Confederate Army of the Potomac. The two armies were separated and Beauregard was already at the scene of the upcoming battle and had crafted a plan of battle. When the two armies combined Johnston assumed overall command, as he was the senior general. When Beauregard explained his plan, Johnston allowed him to implement it and in essence passed the command of the troops to him. Therefore, Beauregard is remembered as the commander of the Confederate Army on July 21, 1861.
Both of these generals were on the field that day, and both can rightly be called the commander.
These Generals were among the best the Confederacy had.
At First Bull Run the Confederates were led by BGen Joe Johnston and BGen P.G.T. Beauregard.
At the Second Battle of Bull Run they were led by General Stonewall Jackson.
General Thomas J. Jackson, also known as Stonewall Jackson.
Irvin Mcdowell
The Confederate general at the First Battle of Bull Run was General P.G.T. Beauregard.
Irvin McDowell
The north realized the First Battle of Bull Run wouldn't be easy
The Battle of Vicksburg.
Confederate General PT Beauregard commanded the Army of the Potomac and General Joseph Johnston commanded the Army of the Shenandoah at the first Battle of Bull Run.
Joe Johnston and PTG Beauregarde.
The Union commander was General McDowell. The Confederate commander was General Beuregard.
Robert E. Lee
At the first Battle of Bull Run the Confederate commanders were PT Beauregard and Joseph A. Johnston. At the second Battle of Bull Run the top Confederate commander was General Robert E. Lee.
Joseph E. Johnston and PGT Beauregard of the Confederate States of America took on Irvin McDowell of the Union forces.
In the First Battle of Bull Run, which took place July 21, 1861 had two Confederate Commanders. They are Joseph E. Johnston and P.G. T. Beauregard. In the Second Battle of Bull Run which took place August 28 through August 30th, 1862 had one Commander. He was General Robert E. Lee.
The main Confederate commander at the second battle of Bull Run was Robert E. Lee. He was assisted by among others by Generals Longstreet and Jackson.
I am pretty sure it was Thomas "Stonewall" Jackson.
The battle was Bull Run (Manassas), and the Confederate commander was Joseph E. Johnston, who ceded some authority to P.G.T. Beauregard on account of the latter's close knowledge of the terrain.
The First Battle of Bull Run aka First Battle of Manassas.
First Battle of Bull Run - 32-34,000 Second Battle of Bull Run - 50,000
Stonewall Jackson