Albion bounced back from falling behind to a fifth-minute strike from Matt Mills to grab their first win in four games.
Thomas equalised on the half-hour with the former Arsenal winger grabbing his second after 65 minutes before Youssouf Mulumbu helped himself to Albion's third three minutes from time.
It was rough on Reading who had won two of their previous three away games - their only victories so far this season.
They had looked set to hold on for a point thanks to the second-half heroics of goalkeeper Adam Federici.
He denied Chris Wood, Gianni Zuiverloon and Marek Cech with stunning saves.
But Federici was powerless to prevent Thomas completing his brace when he made no mistake from 14 yards to convert a cross-field ball from Wood.
Albion got off to the worst possible start when they lost striker Roman Bednar who was stretchered off with a knee injury after just five minutes and then fell behind 60 seconds later.
They were guilty of playing a part in their own downfall as Mills was allowed the freedom of the penalty area. He faced virtually no competition when he rose to head home a left-wing free-kick from Brian Howard.
Reading should then really have doubled their advantage five minutes later only for the unmarked Jobi McAnuff to volley over the bar from just six yards.
Albion took some time to get to grips with falling behind and losing Bednar but battled their way back on to level terms thanks to the pace of Thomas and another error by McAnuff.
Thomas raced on to a misplaced pass from McAnuff and surged past Federici who had raced out of his area to try and intercept.
Thomas still had to hold off the attention of the former Albion loanee Shaun Cummings but once past him he had the simple task of pushing the ball into an empty net before going on to cap a man-of-the-match display with his second.
Mulumbu then struck with a looping volley from the edge of the area to seal Albion's success.