I have two thoughts on this. First is that it may be easier or more natural to do the integration work via the pre-existing Java classes. You didn't mention what the other system was using so there isn't much to go off of. I'm not sure how you normally get server systems to interoperate but there are a variety of interchange methods including SOAP, XML-RPC, CORBA, invent-your-own-language. Most of my work uses the standard Lotus Domino RPC so I can't speak to the efficacy of these new-fangled XML based interop methods.
Now on to the perl part. My guess is that there's a C or C++ API to your database as well. My first inclination would be to write some XS code to access the C api. Second would be to use the C++ api (only because I haven't tried C++ XS yet). The issues you run into here are generalized to your skills with C and C++ and whether it will be any good or not. XS works great and it's how many of the fancy modules on CPAN work. XS is also ugly and you need to somewhat familar with Perl's internals.
So here's a third idea. Consider Inline::Java, Inline::CPP or Inline::C. Some smart people have done all the magic work up front so you don't have to. The Inline::Java module is marked as very alpha and is something I'd use for an project I'm responsible for. The other Inline modules are more mainstream and are more likely to eat your dog and sell your cat. They're probably worth your time (again assuming you are going to use the C or C++ integration options I'm assuming you have around)
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