"I am going to sound like a grumpy old man but that young man shouldn't be in the tournament," said Murphy.
"It is not fair, it is not right."
Si fell off the main tour at the end of last season and entered the 128-man tournament in York as an amateur top-up in the field.
He looked as if he had blown his chance, having surged in front only to miss the final blue in the seventh frame.
Murphy, beaten in the World Championship final by Mark Selby earlier this year, hit back by winning four frames in a row - but a missed blue of his own from the penultimate red cost him the match, which finished close to midnight.
An angry Murphy vented his fury afterwards by telling BBC Radio 5 Live: "I feel extremely hard done by that I have lost to someone who shouldn't even be in the building.
"I don't know why we as a sport allow amateurs to compete in professional tournaments. This is our livelihood. This is our living. We are self-employed individuals and not contracted sportsmen. We don't play for a team.
"The other 127 runners and riders in the tournament, it is their livelihood too. It is wrong, in my opinion, to walk into somebody who is not playing with the same pressures and concerns I am.
"He played like a man who does not have a care in the world, because he does not have a care in the world. It is not fair, it is not right.
"I am not picking on him as a young man, he deserved his victory. Amateurs should not be allowed in professional tournaments, the end.
"This is our livelihood. This is how I put food on the table. This is how I earn money. Since turning professional at 15, I have earned the right to call myself a professional snooker player. He hasn't done that. He shouldn't be on the table."
