yes, map service supports joins. If it doesn't work for you then there must be some other issues going on... if problem persists, maybe a good idea to check with Esri Support.
When I try to publish a map service the join does not work.
also, would you mind describe a bit more on what exact is not working? another question - are you adding the service as a 'map image layer' (aka map service layer') in your web app or adding individual layer off the map service as 'feature layer' in your webmap?
thanks