But now I would like to know if is there a template or model for documenting system requirements when using Agile methodology like Scrum.
There is no template for Scrum because Scrum isn't prescriptive about the way to capture requirements and let you use whatever is appropriate in your context. Many (web) teams are using User Stories and it works well for them but there is no general consensus. Just in case, the recommended template for user stories is:
"As a <type of user>, I want <some goal> so that <some reason>."
But nothing forces you to use stories and they are not appropriate for all projects (e.g. Jeff Sutherland said he will never use stories again for PDA projects, UI and navigation rules are too complex for stories).
With Scrum, I'd say that the general principle is to produce just enough (and just in time) specifications (which is different from an exhaustive use case model in a RUP like approach though). It's up to you to find out what format is appropriate for your context.