I suppose that, when the war was ongoing, Clausewitz was still too young to acquire any relevant position to command a division against Napoleon, but i assume that he could at least be delegated to accomplish minor functions or be charged with the control of smaller military units. So, have they ever been opposed against one another in a battle?
This is a good question for our 'Short Answers to Simple Questions' thread.
Briefly, the major battles in which Bonaparte and Clausewitz both fought were:
Borodino, where Clausewitz was Quartermaster General to Russian First Cavalry Corps under Uvarov. In this capacity he fought on the Russian right wing, participating in an attack against a body of Imperial infantry and cavalry, who retreated from Russian artillery fire after a series of charges fizzled out. This had the effect of stalling the commitment of the Young Guard, which was about to go into action in the center.
Lutzen, where he was the Russian liaison with the Prussians and took part in several cavalry charges, sword in hand; he was wounded behind the ear by a French bayonet.
Bautzen, in the same capacity.
Ligny, where Clausewitz served as chief of staff to Prussian Third Corps, commanded by Thielmann. The corps was not heavily engaged that day, which swirled around the villages of St. Armand, St. Armand-La-Haye, and Ligny in the west, but was present at the battle.
In 1806, Clausewitz was an adjutant in a battalion commanded by Prince August; they fought at Auerstadt, opposite Davout, while Bonaparte commanded in person at Jena to the south. Much reduced, the battalion was captured at Prenzlau during the pursuit.
In the Fall Campaign of 1813 and subsequent operations, Clausewitz served in Wallmoden's corps in northern Germany, which did not partake in any of the battles against Bonaparte in person.
You can read more about all these battles and the soldier who fought in them in Donald J Stoker's biography, Clausewitz: His Life and Work.