It does not seem to be possible to do this using standard Eclipse's export as runnable JAR (right click project -> Export -> Runnable JAR file -> Save as ANT script). However, Eclipse allows you to store the definition of your export as an Ant file, that one can modify later on.
The modification can look like below (I marked the modified parts with comments; it should be easy to compare with a script that your Eclipse generated).
<target name="create_run_jar">
<jar destfile="/mytargetlib/myjar.jar">
<manifest>
<attribute name="Main-Class" value="Main"/>
<!-- Here we only add lib/properties, the rest should be pre-generated by Eclipse -->
<attribute name="Class-Path" value=". lib/myjar1.jar lib/myjar2.jar lib/properties"/>
</manifest>
<fileset dir="/bin" excludes="**/*.properties" />
</jar>
<delete dir="/mytargetdir/lib"/>
<mkdir dir="/mytargetdir/lib"/>
<copy file="myjar.jar" todir="/mytargetdir/lib"/>
<copy file="/myprojectdir/lib/myjar1.jar" todir="/mytargetdir/lib"/>
<copy file="/myprojectdir/lib/myjar2.jar" todir="/mytargetdir/lib"/>
<!-- Again, all the above was generated by Eclipse. We only add a copy of our property file -->
<mkdir dir="/mytargetdir/lib/properties"/>
<copy file="/myprojectdir/properties/mypropertyfile.properties" todir="/mytargetdir/lib/properties"/>
<!-- end of our addition -->
</target>