Retrieving the references in a publication automatically
Both Scopus and Web of Knowledge contain all the information that you need and have APIs that can be used to automate access:


http://info.sciencedirect.com/scopus/scopus-in-detail/tools/api
http://wokinfo.com/products_tools/products/related/webservices/


I have never used them personally, but I hope this kind of information can be accessed using them. Each site indexes articles with their own unique key, so you can use those instead of DOIs if you only need them as unique keys.

Neither of them is free; you can probably access them through your university's subscription though. Be sure to check the usage limits.