I recently had the honor of partaking in a small, intimate wedding ceremony where the reception was to be held weeks later. The Bride and Groom sent out Save the Date magnets for the reception only.
Two possible options for your question:
1. It is perfectly acceptable to send a Save the Date to only those invited to the larger celebration (reception) when there are only a few in attendance at the ceremony.
2. Save the Dates are also wonderful keepsakes. If there are 25 or more at the ceremony, consider sending out two sets- one for the ceremony and one for the reception being held at a later date.
If there are only a few attending the ceremony, one idea might be to hand-create those Save the Dates. Then, everyone will have lovely mementos of your wedding!
In this case I'd suggest you send Save the Dates to the guests you want at your larger celebration after the wedding. If you are planning a small wedding it's likely you are inviting your closest friends and family members to the ceremony. You can easily pass the word to those people personally about your upcoming wedding. By sending the Save the Date to guests not invited to the actual ceremony you're sending them a message early that you look forward to their presence at your celebration.