Consider a simple element, and its associated CSS:
Hover me !
My suggestion is to look at this problem another way: if an element is going to be transitioned when you click on it. Why not just execute your callback on click instead of mouseleave?
I am assuming the tooltip has some connection to the element you mouseenter, in which case mouseleave and click are effectively the same - they both cause mouse pointer to not be over the element anymore (regardless of how browser behaves).
PS: note that in your example, how mouseenter and mouseleave fire also depends on whether you set the transition as default property or as a :hover state property, since this looks like an area where browser vendors are free to optimize as they please, you should probably avoid they in the first place.
transition on #content:hovertransition on #content