Note: I am an Android user so this is not first-hand knowledge.
Per Apple's Japanese Apple Pay page, Apple Pay can be used at all stores where Suica can be used, which is virtually all stores that accept contactless payments in the first place (i.e., you are extremely unlikely to encounter a store that displays one of the other four logos but not the Suica one; the only one I know is my local pharmacy). For reference, however, the five logos to look for are the following:
In order to use the Suica payment feature, you need to install the Suica app and set it up as described here. Note that only iPhone 8 and above (as well as iPhone 7/7+ sold in Japan) can be used to pay in stores. For Apple Watch owners, Series 3 and Japan-sold Series 2 can be used as well.