The deadlock occurred in SQL Server. This is neither Spring, Hibernate, the connection pool nor SQL Servers fault. The problem is that your application is locking rows that either your application, or other applications are also trying to lock (in a deadlock manner).
The easiest fix is probably to have a retry-strategy for your job (just retry the whole transaction if it fails). You could also try to figure out exactly which applications / users were involved in the deadlock by looking at the SQL Server logs.