The final stage was won by Supaksorn Nuntana in 2:05.20 hours, ahead of Jutatip and Chaniporn Batriya.
The 80.40km third stage started from Surat Thani’s City Pillar Shrine and finished at Wat Phra Borommathat Chaiya.
Phetdarin Somrat and Apinya Thiangkaew led for long periods before running out of steam in the final 20km.
Six cyclists, including Supaksorn and Jutatip, were in front before Supaksorn edged Jutatip in the final stretch.
However, Jutatip, who won the first two stages, took the overall title for the second time in a row.
She received the trophy graciously donated by Her Royal Highness Princess Maha Chakri Sirindhorn.
Supaksorn was second overall.
“We met our target. We enjoyed the race very much because there were a lot of teams taking part in the tournament,” said the 32-year-old Jutatip.
“I will soon return to training for the Tokyo Olympics.”
Jutatip, from Roi Et, has competed in two Olympics in 2012 and 2016. She qualified for the 2020 Tokyo Games before the event was postponed until next year due to the COVID-19 pandemic.
Thai Cycling Association president Decha Hemkasri said: “We are very pleased with the tournament. The representatives from the UCI [the sport’s governing body] also are happy with the organising of the tournament and our COVID-19 measures.
“This proves Thailand can organise a tournament in the COVID-19 era.”
The men’s version of the Tour of Thailand was won by German rider Nikodemus Holler last Sunday.