Found that this setting needs to be in the host.json file as Runtime.ServiceProviders.Sql.QueryExecutionTimeout.
This setting must also be in the Configuration for the Logic App. It is not exactly the same though. In the configuration, you must add: ServiceProviders.Sql.QueryExecutionTimeout and specify a time, such as "00:01:00" for 1 minute.
I tested this from 30 seconds up to 3 minutes and it is now working and times out with the Configuration setting. The Microsoft Documentation only has Runtime.ServiceProviders.Sql.QueryExecutionTimeout as the setting, so it is a little tough to find.