Trailing David Law, the 2011 winner, at the halfway stage, Byrne caught him over the morning third round and finished a shot ahead of the Aberdonian.
Despite having arrived late from his Asian Tour commitments, Byrne shot rounds of 67, 66, 63 and 65 for a 19-under-par total of 261, bettering the record set by Peter Smith in 1992 at Murcar by three strokes.
The last man to win the title two years in a row was Elgin's Kevin Stables in 1993/94.
"Hopefully, this will give me the springboard to get my pro career really going. I feel that if I could make it to the European Tour, I could hold my own there," said the 24-year-old Byrne, whose next task is the European Tour Qualifying School Stage 1. If Byrne could carry over his Northern Open scoring exploits to the Q School, he would coast past the barriers between him and the "big time".
He said: "I managed to get two ahead of David [Law] on the outward half of the last round and then got a birdie at the 10th and an eagle 3 at the 11th. That gave me a big enough lead to hold David at bay when he finished strongly, as I knew he would."
Law, winner of the title as an amateur in 2011, had rounds of 63, 68, 65 and 66 for a total of 262, the second-lowest 72-hole aggregate in the tournament's history. "Nine pars on the final outward half really gave me too much ground to make up," said the 22-year-old Law "I would have had to come home in six-under 29, as I did in the first two rounds, to have won." He came close: had he holed a downhill eight-foot birdie putt at the short 18th, it would have gone to a play-off.
The Bookless Trophy for the leading amateur was won by Alexander Culverwell, the Scottish amateur champion from Dunbar. The Stirling University student finished on nine-under 271 and was two shots ahead of the only other amateur to survive the cut, Jamie Savage, the 19-year-old professional's son from Cawder.