Loved Ishiya Japanese Stonegrill when I went there this year for my birthday: http://www.ishiyastonegrill.com.au/
It's on Little Bourke Street. I had the Wagyu stonegrill, myself and my partner were a little over $150 together with drinks, so not cheap, but bloody worth it.
For reasonably priced Japanese, Sapporo next to Mitcham station is fantastic: http://maps.google.com.au/maps/place?sourc...346253128765221