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Simply use /r switch with shutdown command to reboot windows server using command line. Here are various examples of shutdown command.

Restart local system

c:/> shutdown /r

Restart local system with forcefully close running applications using /f command line switch.

c:/> shutdown /r /f 

Restart remote system by specifying system hostname with /m command line switch.

c:/> shutdown /r /f /m \\REMOTE-PC

Add a comment as reason of rebooting system suing /c command line switch.

c:/> shutdown /r /f /m \\REMOTE-PC /c "After Installing Software"