Make sure you've updated your signatures. Edit the sensor (ex all_default), under IPS signatures and filters, +Create New, click "Signature", action drop down Block, Enable, and then in the search type Log4. Click on it and add selected. Did I do that right?
I've already done that. You need to click the "Add Signatures" button in the "Security profiles" section and in the "Instruction Protection" tab, then a window opens with a list of all signatures and you search for "log4j" in the search, click on its line and then add it with the "Use Selected Signatures" button. After that, it will appear in your table of added signatures and by right-clicking on its row you will open a list of applicable functions, including blocking.
Running Fortigate fortiOS 6.2.9 and IPS engine Version 5.00245 and definitions Version 19.00215, the signature is there. As previously stated, I had to set the action to block as the default is default and the default for the signature is pass. It was not greyed our for me.