Nope! SEs can read/see embedded links inside flash, but not follow them. In addition to this, the banner-object must be detectable by the bots. Using something like SWFObect you could have a normal textversion (with link and all) of your add, serving no-flash-browsers and bots.
The nice thing with this method, is that you can have a text-based replacement version of the ad in a <div> that SEs actually can see/index. So if you put your link in this text you will get an inbound link, because the SEs never see the flash-ad. Visitors who has the Flash Player, will get the flash-banner-ad instead of the text-ad.
Look up SWFObject to get more info on the actual implementation.