If you are using systemd then use udisksctl utility with power-off option:
power-off
Arranges for the drive to be safely removed and powered off. On the OS side this includes ensuring that no process is using the drive, then requesting that in-flight buffers and caches are committed to stable storage.
I would recommend first to unmount all filesystems on that usb. This can be done also with udisksctl, so steps would be:
udisksctl unmount -b /dev/sda1
udisksctl power-off -b /dev/sda
If you are not using systemd then old good udisks should work:
udisks --unmount /dev/sda1
udisks --detach /dev/sda