Is it possible to throttle the upload speed of backups?

My daily WHM account backups run at 2am each morning and save to Amazon S3. I run an ecommerce site and I have a couple of order issues around this time where the server has not been able to complete the required processes. I suspect that the backups are sucking the available bandwidth away from the server or in some way using up it's resources because the issues only happen at this time. There are no errors shown in the Apache log or the PHP-FPM logs and the domlogs show that the correct pages were accessed (200 header code), which means that the server was indeed alive. Does anyone know if it possible to throttle the backup bandwidth at all? Thanks