The easiest way to obtain a uncertified electronic PDF document showing the information of your Estonian company shareholders would be via Estonian Business Register free online service.
Log in to the Estonian e-Business Register using your e-resident digital ID card or Smart-ID.
Pick the company you would like to access and click on the company name.
Scroll down to these tabs. Click on PDF icon in the registry tab. This creates a PDF file showing more details than the public registration certificate, including information about shareholders and founders. Starting from 01.09.2021 it does not include beneficial owner information though which is in a separate tab that you can print to PDF.
Alternatively you can also print a lot more data by clicking on print icon in a company view. This generates also a pdf with a lot of extras including shareholders but no beneficial owners. Clicking on PDF icon next to it does not generate a PDF with shareholder information.
For certified paper documents you should contact one of the notaries in Estonia. Estonian Business Register does not issue certified paper documents.
Estonian notaries are also responsible for issuing an apostille to certify the Estonian public records for use in other foreign jurisdictions.
For electronic registration certificate follow the advice here.