The methodology to determine financial aspects of any given transaction is to look at the actual transaction -- what's changing hands, and when, and why -- and from that, we can understand what exactly is happening, and how to relate that to the actual fiqh rulings (such as zakah).
For groceries, the transaction is quite simple. You, the buyer, are purchasing some groceries at some price. The seller agrees to sell you these groceries now, in exchange for immediate payment (cash/debit) or deferred payment (credit card). It's a simple, "vanilla" buying and selling transaction.
The points, then, are not part of the actual transaction. If you didn't have the loyalty card, paid for your groceries, and walked away, we would say that you completed the transaction. There's nothing else here.
So what about the points? In this case, they are considered a gift from the shari'ah's perspective. They're not actually part of the transaction; they're a gift from the seller to the buyer. This applies to similar situations, such as credit-card points (which are a gift from the credit-card company to the card wielder).
What's more, these points are not zakatable. Rasulullah said:
Gold for gold, silver for silver, wheat for wheat, ...
Based on this hadith, scholars have postulated that zakah only applies on cash and currency. (This includes digital cash -- what's in your bank account.) In this case, points wouldn't be considered currency (money, gold, or silver); they would be considered, well, points. So they would not be zakatable.
To explain this hadith a bit further: scholars mention that rasulullah only mentioned two things: gold and silver. Some scholars (a minority) note that both these things are metal, and by extension, postulate that zakah should be paid on all metals -- including iron, steel, copper, etc.
This opinion is a minority. The majority of the ulama say that this hadith means only gold and silver, because they were the currency of the day. Based on this, any currency is zakatable, including USD, CAD, GBP, et. all.
And Allah knows best. If you want to play it safe, you can always cash out your points on your hawl date and pay zakah on your savings. 2.5% really is very little, and you usually don't feel the pinch.
Source: Weekend class on Islamic Finance 101