Thomas, who had two punctures, ended the stage in fifth place, but the Welshman stayed one minute ahead of Yates in the general classification of what is the final warm-up race for the Tour de France.
"I knew I had about one minute 20 seconds to lose on Yatesy so at 200 (metres) to go, when they started sprinting for the win, I was relieved," Thomas was quoted as saying by the BBC.
"I can rest a little bit now and wait for July. This is a confidence booster for the Tour."
Team Sky also won the team event, finishing seven minutes, 18 seconds ahead of UAE Team Emirates.
(Reporting by Simon Jennings in Bengaluru, editing by Ed Osmond)
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