The following plist (Source) needs to be edited. I suggest 'duplicating' the file first, so you will have a backup if needed.
~/Library/Preferences/com.apple.LaunchServices/com.apple.launchservices.secure.plist
If you have Xcode, you can just open/edit the plist directly (not in the scope of this answer), but if not, it needs to be converted from binary to XML format since textedit can't open it as-is.
To convert it into XML, use the following command (Source) in terminal.
plutil -convert xml1 /Users/$USER/Library/Preferences/com.apple.LaunchServices/com.apple.launchservices.secure.plist
Open the file and then search (CMD+F) for skype
or <string>tel</string>
Either delete the following structure, or edit it, by commenting it out using <--!
and -->
at the top and bottom of the <dict>
(Source)
Before:
<dict>
<key>LSHandlerPreferredVersions</key>
<dict>
<key>LSHandlerRoleAll</key>
<string>-</string>
</dict>
<key>LSHandlerRoleAll</key>
<string>com.microsoft.skypeforbusiness</string>
<key>LSHandlerURLScheme</key>
<string>tel</string>
</dict>
After:
<!--
<dict>
<key>LSHandlerPreferredVersions</key>
<dict>
<key>LSHandlerRoleAll</key>
<string>-</string>
</dict>
<key>LSHandlerRoleAll</key>
<string>com.microsoft.skypeforbusiness</string>
<key>LSHandlerURLScheme</key>
<string>tel</string>
</dict>
-->
Save the file and reboot.