Based on the format of the output I suspect that the log output shown above is actually produced by JUL (java.util.logging) and not by log4j.
It is possible to route calls made to the java.util.logging API to the log4j2 implementation. Your log4j2 configuration (which looks correct) should then filter out WARN-level log events emitted by any class in the org.glassfish.jersey.servlet
package.
This involves adding a few more jars to the classpath: see the FAQ.