Colombian Echavarria is aiming for his second victory on the PGA Tour after winning last year in Puerto Rico. Thomas has won 15 times, but is without a success in two-and-a-half years since winning the 2022 PGA Championship.
Max Greyserman, looking for his first PGA Tour win, carded a 64 on Saturday and is three strokes back. Three more Americans are six behind and still in the mix: Kevin Yu (66), Rickie Fowler (67) and Nate Lashley (63).
"I mean, that's the way you want to finish a round," said Echavarria, who hit a five-wood to two feet for the tap-in on the 550-yard hole.
"I had a good tee shot, hit a really good second shot and finished with an eagle. I prefer that than a birdie obviously."
The 30-year-old saved par on the 12th with a difficult downhill chip from thick rough on his third shot, and then dropped a clutch putt.
It might have saved his round.
"I started getting shaky on the back nine with a bogey on nine and an incredible save on 12," he said.
"But we finished the round as well as we could."
Echavarria is 17 under at the Narashino Country Club, located about 50 miles (80.5km) outside central Tokyo.
Thomas won his first major in 2017 — again the PGA Championship — and rose to world No.1 in 2018. Now he's trying to recapture the feeling.
"It's obviously tough," he said.
"It's hard to win at any stage, doesn't matter who you are.
"At the end of the day it has been a while, but I've still won a pretty good amount of golf tournaments. I know how to win. It's just a matter of executing and doing it and that's really been the biggest difference."
The pre-tournament favourites are already out of contention.
Defending champion Collin Morikawa (70) is 13 off the pace, as is Xander Schauffele (68).
Japan's Hideki Matsuyama had a 66 — his best round of the tournament — but is 15 behind.
Australia's Min Woo Lee is one shot better off at three under after carding his third straight 69.
With AAP.
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