Thomas, 30, will join Tour de France champion and Team Sky colleague Chris Froome who is favourite to win the 54.5km event.
Neither achieved a medal in Saturday's road race which was marred by crashes, one of which involved former Olympic track champion Thomas who finished after a heavy late accident.
Australian Richie Porte, a former team mate of Froome and Thomas, and Italian Vincenzo Nibali were two of the casualties who will miss the time trial on the hilly Grumari circuit alongside Rio's coastline.
"I'm thrilled to represent my country in a second event in Rio, the circumstances surrounding my inclusion are unfortunate and I'd like to wish all those who withdrew through injury a quick recovery," Thomas said in a British team statement.
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"I lost quite a lot of skin in my crash and my hip took a pretty big knock, but other than that my legs are feeling good and I'm looking forward to racing again on Wednesday."
(Reporting by Martyn Herman, editing by Neil Robinson)
