Arnold's account of this debate (in Russian) is here: http://www.mccme.ru/edu/index.php?ikey=viarn_burbaki&post=25742517_1256 and here http://vivovoco.rsl.ru/VV/PAPERS/NATURE/BURBAKI.HTM
Let me translate few words from the beginning.
Serre challenged me with this motivation: "I wanted to tell about the influence of Bourbaki on mathematics. If everyone will speak the same, especially panegyrics, this will be boring. Thus I started to search who would express an opposite opinion to mine. After having leafed through the list of mathematicians of the world, I understood that this must be you."
The duel happened on 13 of March 2001 in Institute Poincare.
Then he describes Serre's speach and his own. Published version of Arnold's talk during the debate is called "Mathematics and Physics: a parent and a child, or sisters?" English translation: Physics-Uspekhi, 1999, 42, 12 1205-1217.
Here is a free version: http://ufn.ru/en/articles/1999/12/c/
My impression is that I also read Serre's talk somewhere. But I cannot find any trace of it in the Internet.