I did try and attack him in the way Lilith suggested, but it did not work. Funnily enough, I went and completed a few other side missions and then thought I'd come back and try again, and when I got back to the area where Ozimus was, he was actually waiting in the middle of the camp and this time when he fled, he went down to the next level as he's supposed to do and I was able to defeat him.
Interesting that he got stuck in that way, but I'm just happy that it seemed to "reset" itself after a while?