How to deploy heroku app with secret yaml configuration file without committing the file?

Heroku have some guidance on this -

http://devcenter.heroku.com/articles/config-vars

An alternative solution is to create a new local-branch where you modify .gitignore so secret-file can be pushed to heroku. DON'T push this branch to your Github repo.

To push non-master branch to heroku, use:

git push heroku secret-branch:master

More info can be found on:
https://devcenter.heroku.com/articles/multiple-environments#advanced-linking-local-branches-to-remote-apps

Use heroku run bash and then ls to check whether your secret-file have been pushed on to heroku or not

Store the s3 credentials in environment variables.

$ cd myapp
$ heroku config:add S3_KEY=8N029N81 S3_SECRET=9s83109d3+583493190
Adding config vars:
  S3_KEY    => 8N029N81
  S3_SECRET => 9s83109d3+583493190
Restarting app...done.

In your app:

AWS::S3::Base.establish_connection!(
  :access_key_id     => ENV['S3_KEY'],
  :secret_access_key => ENV['S3_SECRET']
)

See the Heroku Config Vars documentation which explain development setup etc.