Gabyta88
You have to get the ticket for the SBB IC train in Switzerland from SNCF in France. They will issue a paper ticket for the Swiss railways part.
Again, it is clearly stated on their train booking page when you buy tickets for Switzerland with SNCF, see point 2:

There is no way to retrieve the SNCF ticket in Switzerland. You will have to pay for a new ticket with elevated surcharge if you travel with a booking code from SNCF on an SBB train as you are considered a passenger without valid ticket.
It would have been more convenient to buy a ticket to Basel SBB with SNCF, and the Swiss stretch with SBB. Or, the entire journey with SBB (www.sbb.ch/en).
Kind regards,
Roland