Ocon was the last driver to stop during the race, doing so as he commenced the final lap.
Photographers and officials were milling in the fast lane while parc ferme barriers had been erected.
Meanwhile, Ocon approached at terminal velocity before slowing to avoid those in the lane.
Following the race, the event stewards investigated the incident and found the FIA had breached two articles of its own International Sporting Code.
In response, the FIA resolved to examine its protocols and issued an apology to Ocon.
“The FIA has apologised,” the Frenchman told Sky Sports.
“They assured us that this is not going to happen anymore. Thank God nothing happened, and so all good from now.
“We are racing at the time. It's, of course, normal that there shouldn't be anyone in the pit lane until after we are racing like that.
“These things are normally not going to happen, the FIA has assured us that they are making sure they are changing the protocol and making sure there is no one in the pit lane until the end, so I'm confident we will not see that anymore.”
Ocon had started the Azerbaijan Grand Prix from the pit lane after Alpine opted to change his set-up following qualifying.
It proved a double-whammy as, by removing the car from parc ferme conditions, it had to start Saturday's F1 Sprint from the pit lane too.
Ocon finished last Sunday's race in 15th, ahead only of Logan Sargeant.