First off, the data on the last World Cups show that during the knock out stage, there are substantially fewer goals scored. This makes sense: from tomorrow it's make or break. This wasn't too difficult to deal with, though $-$ we just needed to modify the distribution for the zero component of the number of goals ($\pi$, as described here). In this case, we've used a distribution centered on around 12% with most of the mass concentrated between 8% and 15%.
These are the predictions for the 8 games. Brazil, Germany, France and (only marginally) Argentina have a probability of winning exceeding 50%. The other games look closer.
Technically, there is a second issue, which is of course that in the knock out stage draws can't really happen $-$ eventually game ends either after extra time, or at penalties. For now, we'll just use this prediction, but I'm trying to think of a reasonable way to include the extra complication in the model; the main difficulty is that in extra time the propensity to score drops even further $-$ about 30% of the games that go to extra time end up at penalties. I'll try and update this (if not for the this round, possibly for the next one).