World champion Trey Hardee claimed silver, 198 points behind in a United States one-two and Cuba's Leonel Suarez secured a second successive bronze thanks to an Olympic best performance for the decathlon of 76.94 metres in the javelin.
Eaton had virtually sealed the gold medal after nine of the 10 events but after dragging himself around the concluding 1,500 metres in a time of four minutes 33.59 there was only relief on his face.
"The one-two was what we really wanted," Eaton said.
"Trey and I are doing our best to carry on the great history of decathletes," he said before adding that winning the gold had been harder that setting the world record of 9,039 during the US trials in June.
"Decathlons in the States are so much easier because of the time frame, I think I competed in Eugene for the world record at total of 13 hours and that's just what we competed today and yesterday was a 12ish hour day so this was way harder."
The 24-year-old had a cushion of 151 points going into the race and was content to stay in the pack, not bothering to follow when Belgian Hans van Alphen upped the pace.
Eaton caught his breath and was congratulated by the other decathletes. They then started the customary joint celebrations, posing for a group photo - Eaton draped in the US flag - before setting off on a lap of honour together.
"I'm proud of Ashton and I'm looking forward to the next few years with him," twice world champion Hardee said.
"I've been the best in the world for a couple of years and it's safe to say that my reign is over.
Having broken Roman Sebrle's 11-year-old world record this year, Eaton missed out on taking the Czech's Olympic mark of 8,893 by 24 points.
He had started the second day with a lead of 220, only to be pegged back to 99 points by Hardee after a poor discus. However, Eaton took control again with third place in the pole vault of 5.20 metres and a personal best of 61.96 in the javelin.
He was helped in the pole vault by the failure of Hardee's gamble of passing at 4.90 and going straight to 5.00.
Wearing a support on his right elbow following surgery last year, Hardee knocked the bar off on all three attempts, leaving him with a best of 4.80 and allowing Eaton to stretch his lead.
He had been left shaking his head at the end of the discus after only managing 42.53, almost five metres down on his personal best for 22nd out of the 27 athletes.
Hardee, the stronger thrower of the US pair, had finished third in the discus with 48.26 for 834 points, 118 more than Eaton's mark earned, to close the gap on the leader.
"I threw a terrible one, he threw a bad one and I was like 'all right, we're doing okay'," Eaton said.
"I threw another bad one, he threw an awesome one and it was: 'oh I have to figure out what I'm doing and do this' and I threw another bad one. I was so disappointed with myself... he competed well. I didn't."
Hardee also beat Eaton in the day's first event, the 110 hurdles, shouting as he crossed the line in a personal best time of 13.54.
Eaton had got his first Games off to a flying start on Wednesday with the fastest 100 metres in an Olympic decathlon of 10.35 seconds. He then won the long jump with 8.03 metres before going close to his personal best in the shot put with 14.66.