The bizarre incident happened early in the match with the West Africans already trailing 1-0 to Australia.
Television replays showed that a shot by Australian forward Leena Kharmis hit the post and rebounded to Equatorial Guinea defender Bruna, who apparently believed that play had been stopped.
After holding the ball for at least three seconds, she let it fall to the ground but Hungarian referee Gyoengyi Gaal waved play on amid Australian protests and general incredulity.
The West Africans equalised shortly afterwards but Australia went on to win 3-2.
FIFA mentioned the incident in a report on their website and German magazine Kicker said a FIFA official had apologised at the post-match media conference.
"We all know that there was an incident. We have spoken to the referee. She said that she's very sorry for not seeing such a clear handball," match official Karen Espelund was quoted as saying.
FIFA are currently studying the use of technology to be used when it is not clear whether the ball has crossed the goal-line but this would not apply to penalty area incidents such as the one on Sunday.
A number of competitions are now using two additional linesmen behind the goals to help the referee spot penalty area incidents but the Women's World Cup is not among them.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.