Unmarked centre-back Matthew Mills grabbed his second goal in Reading colours with a downward header after just six minutes of Saturday's game.
But Thomas, returning from a three-match suspension, capped a man-of-the-match display with a brace to end a three-match winless streak for the promotion-chasing Black Country outfit.
The Albion winger capitalised on a short back pass from Jobi McAnuff to grab his first midway through the first half.
And with Royals goalkeeper Adam Federici producing a one-man show after the interval to seemingly keep the scores level, Thomas kept his cool when put clean through to put the hosts in control.
Youssouf Mulumbu then volleyed a stunning third late on to put a gloss on the scoreline and send the majority of a 20,935 crowd home happy.
Roberto Di Matteo's pre-match tactics were thrown into disarray after just five minutes as striker Roman Bednar was stretchered off with a lower back injury, youngster Chris Wood taking his place.
And if the opening five minutes were bad enough for Albion then the next 30 seconds were even worse as Reading snatched an early lead through the unmarked Mills from six yards.
The Baggies were slow out of the blocks but Reading could count themselves somewhat fortunate after 13 minutes when Luke Moore found himself clean through before being cruelly upended by Ivar Ingimarsson.
Referee Anthony Taylor awarded a free-kick on the edge of the area but controversially failed to show a card of any colour to the Icelandic defender.
Reading were content to sit back and knock the ball around after grabbing an early opener but their approach changed just before the half-hour mark as Thomas pulled Albion level.
A Royals corner was cleared to the halfway line where McAnuff attempted to find Federici, who was a long way out of goal, with a back pass which was interrupted by Thomas.
The summer signing nipped in to lob the ball over the visiting keeper before outpacing a backtracking defence to put the ball over the line from close range and ensure an eventful first half came to a close at 1-1.
But Federici kept his side on level terms shortly after the restart with a stunning save to keep out Wood's acrobatic effort at the far post.
Albion were turning the screw in the second half and looking to capitalise on an uneasy performance by visiting full-back Shaun Cummings - who spent a spell on loan at The Hawthorns earlier this season.
Despite a string of great saves from Federici it was only a matter of time before the hosts went ahead and it was the lively Thomas who came up with the goods.
Seventeen-year-old substitute Wood weighted a perfect throughball for the winger and he finally got the better of the shot-stopper with a cool finish.
Federici again kept Albion in check after their second but he was powerless to stop Mulumbu's goal - and Albion's third - from 20 yards.