I need to create a callto:// link that will dial phone # then pause and dial DTMF ext number.

Example callto:// Skype number + pause + ext

Please let me know how can I do this. I didn't find any reference in Skype documentation.

For the time being, you cannot. Callto only supports "real" phone numbers.

However in case you're writing an application, then you can use Skype API to dial the "real" number, and when the call becomes IN PROGRESS, you use SET CALL <id> DTMF <value> to send the dialtones.