Runner-up to Jamie Donaldson in Abu Dhabi last week, Rose had to be content with a four under par 68 after he was penalised a foot from the hole on the short 17th.
England's world number four had missed his birdie attempt and was addressing the ball ready to tap in when he noticed it moved a fraction.
European Tour referee Paul Carrigill, himself a former player on the circuit, was called and with no wind to blame for the change in position he imposed the extra shot and told Rose to move the ball back before continuing.
Rose's next dropped stroke was all of his own making, though.
His second to the long first after he had turned in 34 was fired miles right into the desert scrub and it took him three more shots to make the green.
A five-foot putt limited the damage to a bogey six and on five under he was still only two behind the joint leaders - Alexandre Kaleka, Santos, Garth Mulroy, George Coetzee, Marcus Fraser and Martin Kaymer.
Coetzee was producing the most action-packed round. He resumed with a double-bogey seven, but had six birdies in seven holes around the turn.
After the shock of his missed cut in Abu Dhabi last Friday Tiger Woods returns to the scene of his last major win, five years ago, this week.
Torrey Pines near San Diego, the venue for the Farmers Insurance Open, is where Woods has claimed six more of his 74 PGA Tour titles and before that six world junior titles between the ages of eight and 15.
When told the 37-year-old world number two had an average of 68.6 in nearly 50 Tour rounds at the venue, defending champion Brandt Snedeker said: "That's just phenomenal -- I mean, that's stupid."