As Scotland, Canada and Sweden jointly set the pace with 10-under-par rounds of 62 in the four-ball better-ball format, Duval incurred a two-stroke penalty for taking an illegal practice putt after completing the 16th hole.
The penalty was carried forward to the next hole, the short 17th, which Duval birdied but was then forced to record a bogey four while Woods’s par three was the counting score for the U.S. team.
Duval said of the incident: “I wasn’t aware, verbally we were not told. Thankfully, it only cost me one shot.”
The Americans, who carded a 66, are hot favourites to win the title for the third year running, and for the sixth time in nine years.
Woods said he had been out of touch during the round: “I wasn’t swinging well and I definitely wasn’t putting well. Add those two things together and you’re not going to shoot low scores.
“But we are in great position, only four back with two rounds of alternate-shot to play.”
The world number one made just three birdies and had trouble off both the tee and on the fast, undulating greens at the Taiheiyo Club in Shizuoka.
His day was summed up by a scrambled par save at the par-four eighth after he badly missed the fairway with his driver.
“We ham-and-egged it pretty well today,” said Woods.
Scotland’s Andrew Coltart and Dean Robertson produced a 10-under-par 62 to join Swedes Niclas Fasth and Robert Karlsson and Canadians Mike Weir and Ian Leggatt at the top of the leaderboard in the $3 million event.
“We would probably have settled for six-under but 10-under is a bonus. We combined very well and I think both teams were feeding off one another today,” said Robertson, who made four birdies on the front nine and three more after the turn.
Karlsson holed two eagle putts, at the sixth and at the last, where he made a 20-foot putt.
Meanwhile, Spain’s Sergio Garcia made birdies on the last four holes as he and partner Miguel Angel Jimenez finished with a score of nine-under 63 to tee off in Friday’s foursomes one shot off the pace.
New Zealand’s Michael Campbell and David Smail also combined well for a 63.
“After the ninth, we said we needed to get something going. We missed a lot of birdie chances in the beginning but it was great to finish that way,” said Garcia, who has won twice on the U.S. Tour and once in Europe this year.
Highly-fancied South Africans Ernie Els and U.S. Open champion Retief Goosen, the second seeds, finished a further shot back on eight-under.
Ireland’s Padraig Harrington and Paul McGinley, first and second respectively in the Volvo Masters last week in Jerez, also carded a 64.
The Japanese pairing of Toshimitsu Izawa and Shigeki Maruyama delighted their home fans with a return of 64 as well.
First round scores:
62 Scotland (Andrew Coltart/Dean Robertson), Sweden (Niclas Fasth/Robert Karlsson), Canada (Mike Weir/Ian Leggatt)
63 Spain (Sergio Garcia/Miguel Angel Jimenez), New Zealand (Michael Campbell/ David Smail)
64 Ireland (Padraig Harrington/Paul McGinley), South Africa (Ernie Els/Retief Goosen), Japan (Toshimitsu Izawa/Shigeki Maruyama)
65 Denmark (Thomas Bjorn/Soren Hansen), England (Ian Poulter/Paul Casey)
66 Zimbabwe (Mark McNulty/Tony Johnstone), Fiji (Vijay Singh/Dinesh Chand), Australia (Adam Scott/Aaron Baddeley), Wales (Phillip Price/Mark Mouland), Malaysia (Danny Chia/Periasamy Gunasegaran), Mexico (Octavio Gonzalez/Alejandro Quiroz), United States (Tiger Woods/David Duval)
67 France (Thomas Levet/Raphael Jacquelin), China (Zhang Lian-Wei/Liang Wen-Chong), Phillipines (Rodrigo Cuello/Danny Zarate), Argentina (Angel Cabrera/Eduardo Romero), Norway (Per Haugsrud/Henrik Bjornstad) 68 Paraguay (Carlos Franco/Angel Franco) 70 Netherlands (Maarten Lafeber/Robert Jan Derksen)—Reuters