They made off with a substantial sum of cash after locking him in an upstairs room. He managed to free himself a short time later and raise the alarm.
Fellow priest Fr Brian White said it was the third time in two and a half years that the house had been robbed.
"This is the first time that Fr O'Dwyer was in the house when it happened," he said.
"There were a few different collections, people had given to needy causes that he had kept locked away.
"It was just unfortunate that they were there in the house at the time."
The money taken included charity donations and parish wages.
The priest, who is in his 50s, was not injured.
The robbers are believed to be in their late teens and spoke with local accents.
The parochial house belongs to St John's Church on the County Garvaghy Road.
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(Source: PT)