Thomas' tied second is the best finish ever by an Indian in the 10-year history of the Championships.
The Dubai-based golfer (4-under 66) ended two shots behind the winner, Takumi Kanaya (65), who made a great charge between the 14th and 16th with three successive birdies to surge ahead to victory over Thomas and the Asian Games individual gold medallist fellow Japanese Keita Nakajima (67).
The 20-year-old Kanaya, who was second individually at the World Amateur Championships last month days after being part of Japan's Asian Games gold medal winning team, totalled 13-under 267.
Thomas and Nakajima were 11-under 269 as the threat of lightning stopped play for an hour and 11 minutes at the new Tanjong Golf Course.
While Kanaya earned the coveted spots into the 2019 Masters and the 2019 Open Championships, both Thomas and Nakajima saved a place at the final stage of the Open Qualifying Series.
Overall, it was India's best-ever Asia-Pacific Amateur Championships with five of the six Indian players making the cut this week.
Thomas was followed by debutant Kartik Sharma (70) Tied-13, despite a bogey-bogey finish.
"I am very proud and thrilled with the finish and I know I can compete with the best," said Kartik, who plays at the DLF.
Yuvraj Sandhu (71) also dropped two shots in last four holes and ended Tied-25, while Kshitij Naveed Kaul (67) was Tied-38th and Varun Parikh (74) was tied 57th.
Thomas fought back from a disappointing 4-over on the first day and was the only player in the Top-6 to have an over par during the week. With 64-65-66, he was 15-under for last 54 holes.
"This medal (second place) means a lot to me. That 4-over on first day was pretty disheartening but I am very proud to have fought back from there and come so close, Thomas said.
"I knew I was one shot behind (Nakajima) around the 12th and I still felt if I could get that birdie on 17th, which I missed, at 12-under I would have a chance (against Kanaya). If I had got that I would have gone for a birdie on 18th, too. Also the bogey on 15th cost me heavy," he added.
Overnight leader and defending champion, Lin Yuxin (75) had a disappointing day as he slipped to Tied-9th.
Filipino Lloyd Jefferson Go (69) was fourth in his last event as an amateur, while Thai KK Limbhasut (69) was fifth and 2015 AAC champion Cheng Jin (70) who shared the lead after first two days, was sixth. Another big hopeful, China's Andy Zhang, second last year, ended T-13 after a final round of 73.
Kanaya started the day in Tied-3rd and two shots behind overnight leader and defending champion. For a better part of the round, Nakajima held the lead as he was 4-under through first 10 holes.
Kanaya, 4-under through first eight, dropped a shot on eighth but after the turn the tide, too, turned. Kanaya's three birdies in a row from 14th sealed the issue.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)