Zane Scotland, who hit the first shot of the tournament which marks a new chapter in the Tour’s history with the introduction of the world ranking points, and Craig Hinton shot identical rounds of five-under par 67s to hit the front.
Veteran Miles Tunnicliff occupied solo third with a four-under par 68, followed by a group of eight men tied for the fourth place at 69, including Thomas.
It really wasn’t the best of starts for Thomas, who opened with a double bogey six when he overshot the green with a wedge and then three-putted.
But Thomas showed terrific mental strength to make three birdies and turn at one-under, before picking up three more shots on the back nine that contained just one bogey.
“I really played well and made very few mistakes after a disappointing start,” said the 16-year-old reigning EGF Order of Merit champion, who nearly won the Dubai Creek Open last year.
“If I can keep the momentum rolling all the way through, it will be great, but I don’t want to get ahead and will take things as they come.”
Thomas also leads the amateur division by one shot over Abu Dhabi-based Brazil’s Tiago Lobo with Saudi Arabia’s Othman Almulla third on level-par.
Scotland rode on a fluent start to string together a solid round that included eight birdies, with four of them coming in the first five holes.
The 10-time winner on the MENA Tour said: “I made some good putts early in the round and that kind of set the tone for the day.
“Overall, it was a pretty solid round, especially my approaches were very close and that helped me keep going.”
Hinton later joined him on top of the leaderboard, and he also made four birdies in five holes, but unlike Scotland who made them in the beginning of his round, Hinton made his over the closing stretch.
Welsh ace Stephen Dodd, the Scottish duo of Paul Doherty and Daniel Kay, England’s Jake Shepherd, Jesper Alm of Sweden, India’s Manish Goel and Carlos Balmaseda of Spain completed the group tied for fourth on three-under 69.
Three birdies in a row from the first hole highlighted the round of Dodd, a three-time winner on the European Tour, who also topped the MENA Golf Tour Order of Merit in 2012.
Tunnicliff, a two-time winner on the European Tour, picked up four shots in six holes after making opening with a bogey to close out a fabulous front nine of 33. He bogeyed the 11th, before finishing strongly with birdies on the 15th and 17th to move into contention for his maiden Tour title.
The 47-year-old Englishman said: “I played pretty solid golf. Drove the ball well and hit some very good iron shots close to the pin, especially on the front nine. I struggled a little bit on 11, 12 and 13, but managed to finish strongly with two late birdies.”
Andrew Marshall, a two-time winner on the European Tour, returned a two-under 70 to take a share of 11th place.
