Unfortunately there is no such option for SCP, SFTP or even FTP transfers to Amazon S3 (see this Stack overflow post for example).
If you are able to install software on your linux machine, you could use s3fuse to mount your S3 bucket as a filesystem and then just copy the files to that mounted filesystem.
If you aren't able to install additional software on your linux machine at all, you could also launch an Amazon EC2 instance, e.g. a t2.micro instance eligible for the free-tier usage, and transfer your files to S3 via the EC2 instance.