Services athlete Thomas cleared 2.22m to set a meet record while Roy of Jharkhand finished second with an effort of 2.19m. Junior prodigy S Harshith (ONGC) took the bronze with 2.16m.
Thomas tried to obliterate the national record of 2.25m by attempting to clear 2.26m but failed in all his three attempts.
Thomas had won the South Asian Military Championships at Kathmandu earlier this year. Barring his fifth place in the Asian Indoor Championships at Hangzhou, China, he was unbeaten throughout the year and is one of most consistent athletes in the country.
In shot put, national record holder and London Olympian Om Prakash Karhana finished third with a disappointing effort of 17.81m, well below his personal best of 20.69m.
Jasdeep Singh, representing ONGC and a bronze medallist in the Asian Junior Championships four years ago, won the gold with a personal best of 18.14m. Railways' Satyender Kumar was second with 17.85m.
Joseph Abraham, the reigning Asian Games gold medallist who narrowly missed the London Olympics earlier this year, avenged his defeat to Satender Singh in 400m hurdles.
Joseph, who turned 31 yesterday, said he had stopped training after the Asian All-Star competition in Kazakhstan in June. He further added that he will concentrate on 400m race next year and will resume 400m hurdles in 2014.