I'd say
"I made a call to him on/by/via Skype".
Both Skype and the telephone are a system of communication. If "on/over" could mean "using a particular type of machine or equipment" or "by means of", for example, on/over the phone, could you please tell me why it is incorrect to say "I made a call to him on/over Skype"? Thank you gratefully.
I'd say
"I made a call to him on/by/via Skype".
It's also used as a verb- I skyped her.