No, MySQL cannot do this alone, but you can bind unix processes to specific cores in general, see this question on unix.stackexchange and the linux manual concerning taskset, and this can also be applied to mysql processes of course.
But actually I would not try this first. Processes under linux are more or less good distributed. Sticking processes to specific cores removes the possibility to use more cores, if those are available.
I would configure the MySQL instances like Rolando stated in his answer according to the balancing wishes, like set the number of treads in a percentaged manner. And only if this fails miserably I would enforce processes onto specific cores. (Actually at first I would try to merge the two instances into one instance...)
Keep in mind that just because you restrict processes to single CPUs this does not mean the processes will finish in the same ratio you distributed them among CPUs. Accessing RAM, harddisk and available RAM are just some examples of resources, which are not controlled by this change, but all have serious influence on the finishing time of computations. If you want to aggressively change scheduling of resources, you may want to take a look at interfering at those levels too...