Yes, but it wont drop streight in.
You'll need the 6 speed prop from an S4 or 2.5TDIQuattro A4, and you'll probably need to change the rear diff as the 6 speed has a 4.1 ratio and your 2.8 will have 3.8 iirc.
You'll also need the 6 speed gear linkage (not sure if the A6 one will work on an A4) and possibly the engine/tranny spacer from the 2.7 engine.
You may also find you'll need to swap the front driveshafts, as the A4 ones will have smaller inner CV's and the A6 ones might? be too long, although i'm not 100% certain on that.