Hardee, who triumphed in Berlin and Daegu and took Olympic silver behind Eaton last year, was looking off the pace on the opening morning and went into the high jump, the fourth discipline, in fifth place.
With a personal best of 1.99 metres it was among his weaker events but he strained a hamstring in his second attempt and then failed again.
"My hamstring got tight on me in the second jump and just wouldn't release and the third jump came too soon for me to recover," he said. "My body would not let me compete today.
"Gunnar has done outstandingly in the first four events but I still think Ashton is the man to beat," added Hardee, somewhat prophetically, ahead of the day-closing 400 metres.
At that stage 20-year-old Nixon was leading on the back of personal bests in the long jump (7.80 metres) and shot (14.68) as well as recording the day's best high jump clearance with 2.14.
A strong 400m finished a great day for the young American as Eaton struggled with his long jump, shot and high jump.
However, he then showed why he is the world record holder with a storming 46.02 lap of the blue track, the fastest 400m ever run in a world championship decathlon.
It took him to an overnight total of 4,502 points, nine ahead of Nixon and 75 clear of Germany's Michael Shrader, who ended the day on a high with a personal best 47.66 in the 400.
"I couldn't find the motivation but before the 400m the coach said to me 'wake up, it's the world championships. Go into the lead for the second day,' said Eaton.
"And I did it. Now I feel some spark for tomorrow and they are my strong events so I'm looking forward to it."