The D/L premise is that you have resources in wickets and overs with which to make runs. The logic is this: whether you're bowled out or bat 50 overs, you've used 100% of your resources. The trick is in converting the two into an equivalent percentage.
You get bonus runs on the target by way of a significantly less complicated formula that is proportional to the difference in total resources between the two sides. However, That's only if the first team has been robbed of more resources.
Tonight, they hadn't and so the target was a factor of the ratio of resources available to the two teams, the formula that was used is the one usually applied when only the chasing team loses overs. They lost fewer resources than Sri Lanka because they'd already spent their top six before the rain break. When the rain set in, they'd spent two thirds of what they started with and what should have been a 15-20% break was less than 5%. Australia got punished because basically it would have been difficult for them to bat 50 overs, while probably being a little easier for Sri Lanka to chase given the extra time.
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