I think the "use <version number>;" at the top is likely your best bet... or just skip the Makefile.PL altogether - CPAN seems to understand Module::Build-based modules.

(I actually tried to create a new module with Build.PL specifying the minimum perl version, and then asked Build.PL to create the Makefile.PL - seems the Module::Build guys don't know how to do this, either.)