The 30-year-old had been hoping to play a full part in the international break but was ruled out of the game against Wales on Monday.
Republic of Ireland boss Martin O'Neill now has to change his team around at less than 24 hours notice as his side try to qualify for the 2018 World Cup in Russia.
Long played 80 minutes of Friday's qualifier against Moldova and trained on Sunday night but he has failed a fitness test and will now return to Southampton.
While his injury is not thought to be serious, it could see him start Sunday's game against the Magpies on the bench.
Mauricio Pellegrino may decided to start Charlie Austin for the clash at St Mary's, while Manolo Gabbiadini could be pushing for another start up top as he tries to find his form in front of goal.