You might take a look at make.pl (indexed here). It is billed as "make with Perl as the rule language. Write a plain makefile in Perl syntax, or write a program [which] does a few file-dependency driven things." Unfortunately it's written as a monolithic program, but you could probably easily modularize it.

Then there's cons — "a replacement for make. It is not compatible with make, but it has a number of powerful capabilities not found in other software construction systems, including make. ... It is implemented in Perl. You don't need to know Perl to use cons, although you can use it more powerfully if you do." I haven't looked; maybe it has a modular API you could use or extract.