Prefix the encrypted value with {cipher}. Every other property stays as it is, so you can encrypt individual values instead of whole files:

sql.store.user=cm_management
sql.store.password={cipher}48f7940cfb53bb12e1e23399647109d68b4f20d25846cb...
sql.store.url=jdbc:mysql://localhost:3306/cm_management

This file can be committed to Git. The key must not be part of it.