You can use xdotool:
First you should find the id of that window
$ xdotool selectwindow //After you use this line you should select the window
12345678
And you just minimize it.
$ xdotool windowminimize 12345678
xdotool is available as a package in at lease Debian, Ubuntu and Fedora.
And you can install this tool with this line.
$ sudo apt-get install xdotool
Credits:
https://stackoverflow.com/a/26704369/3139930