Dozens of joyous fans scaled fences and ran on to the field at the final whistle to swarm the home players after Jamaica's first-ever win over the USA.
"We can confirm that a warning has been issued against the Jamaica Football Federation (JFF) following the events that occurred after the match between Jamaica and United States," FIFA said in a statement on Thursday.
JFF president Horace Burrell promised to beef up security for future home games.
"They have informed us that if this happens again, very serious sanctions will be taken against Jamaica so let me appeal to spectators not to ever run on to the field," Burrell told Jamaican media.
"If it is felt that invading the field is a threat to the players and the officials, then FIFA would simply ban the National Stadium as a venue for play."
Guatemala, United States and Jamaica are level with seven points from four games in Group A in round three of the CONCACAF region qualifiers. Jamaica's next home match is against Antigua on Oct. 16.