The accepted answer above didn't quite work for me, so here's my implementation.
For context I'm running a Minecraft server on a Linux daemon managed with systemctl. I wanted to be able to send commands to stdin (StandardInput).
First, use mkfifo /home/user/server_input to create a FIFO file somewhere (also known as the 'named pipe' solution mentioned above).
[Service]
ExecStart=/usr/local/bin/minecraft.sh
StandardInput=file:/home/user/server_input
Then, in your daemon *.service file, execute the bash script that runs your server or background program and set the StandardInput directive to the FIFO file we just created.
In minecraft.sh, the following is the key command that runs the server and gets input piped into the console of the running service.
tail -f /home/user/server_input| java -Xms1024M -Xmx4096M -jar /path/to/server.jar nogui
Finally, run systemctl start your_daemon_service and to pass input commands simply use:
echo "command" > /home/user/server_input
Creds to the answers given on ServerFault