France winger Thomas scored two early tries to boost the bid of his joint head coach Laurent Travers to become the first man to win European club rugby's most prestigious trophy as player and coach.
Thomas could have completed his hat-trick but chose to pass the ball over the line to scrumhalf Maxime Machenaud, who added three conversions and two penalties.
Munster, 24-3 down at the interval, fought back with second-half tries by Simon Zebo, Rhys Marshall and Andrew Conway but never looked capable of setting up an all-Irish final against Leinster.
"My whole family was here, we played a great game, the forwards were great. Our first half was nearly perfect even if we lacked a bit of discipline," man of the match Machenaud said.
"Our forwards were so good, it all started from there."
Big-spending Racing, who have never won the European Cup and were runners-up two years ago, will face Leinster in Bilbao on May 12 after the three-times champions swept Scarlets aside 38-16 on Saturday.
In the heat of Bordeaux's Chaban Delmas stadium, Racing went ahead after five minutes when Thomas finished in the corner after good work by the forwards.
Machenaud converted and after Ian Keatley slotted a penalty for Munster, the France scrumhalf converted another try by Thomas who was perfectly set up by Virimi Vakatawa.
Munster could not deal with their opponents' pace and power and fell further behind after a handling error by Alex Wootton allowed the home side to burst through the defence again.
Thomas unselfishly passed the ball to Machenaud, who touched down and converted to give Racing an 18-point lead midway through the first half and he added two more penalties before the interval.
Munster did not capitulate, however, and after Racing were reduced to 14 when Marc Andreu picked up a yellow card for offside, they reduced the arrears with Zebo touching down in the corner after a nice team move before Conway and Marshall claimed late consolation tries.
(Reporting by Julien Pretot; Editing by Ed Osmond)
