you could use dd and your harddrive.
I will give an example:
For the backup (with your rasbian jessy sd card in the reader, but unmounted):
sudo dd if=/dev/mmcblk0 of=/home/bruni/backup.img
For the restore, after you have unmounted and replaced the sd card with a fresh one:
sudo dd bs=4M if=/home/bruni/backup.img of=/dev/mmcblk0
Of course you will first have to verify that mmcblk0 is your sd card (to do this compare the output of
df -h before and after you insert the sd card) and replace bruni with your username.
I use the above for backing up my raspberry pi kodi installation.
PS: Neither copy nor rsync will lead to a bootable sd card, which is what you want.