The American's final-day 65 saw him finish 27 under par to set the record at 253 strokes, while England's Justin Rose was second on 20 under, a shot ahead of American Jordan Spieth.
It was the fourth successive day Thomas, 23, entered the record books in Honolulu.
The world number eight said: "It's been an unbelievable week. Unforgettable."
Thomas started the event by becoming the youngest man to register a sub-60 round on the PGA Tour with an opening 59, and he followed that up by setting the lowest 36-hole total before equalling the record for the 54-hole mark.
His wire-to-wire victory beat the previous lowest 72-hole score of 254, made by American Tommy Armour III at the Texas Open in September 2003.
It was also Thomas' second successive Tour victory after winning the SBS Tournament of Champions, also in Hawaii.
Thomas's two weeks in Hawaii have seen him finish 49-under par.
Thomas made a poor start as he missed a 10-foot putt for par on the fourth, but saved par on the sixth and went on to card four birdies in five holes before tapping in for a birdie on the 18th.
"I was really nervous (before the round)," said Thomas. "I just had a hard time getting in a comfortable mindframe. I felt like I was doing what I needed to do and making some pars, besides that bad bogey on four, but that par putt I made on six was huge."
Rose's closing 64 was enough to finish above Spieth, while Scotland's Russell Knox was tied for 11th on 14-under-par.
"I felt like I was trying to win a tournament for second place," said two-time major winner Spieth.
Justin Thomas set a new record for the lowest 72-hole score in PGA Tour history as he won the Hawaii Open.