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Lloyd's brilliant double in the final was enough for the USA to complete a hat-trick of Olympic Football titles, as the midfielder added to her winner in the Beijing 2008 showpiece.
They also made amends for her penalty shoot-out miss in last year's World Cup final.
Yuki Ogimi pulled a goal back for Japan, who had plenty of chances to equalise and were denied by the woodwork as they failed in a bid to add the Olympic title to their world crown.
But they contributed to a superb spectacle and another brilliant advert for the women's game.
The USA were playing in their fifth successive final, having lost just one of the previous four, while Japan were in their first.
Both sides had come through scares in the semi-finals, the USA coming from behind three times to beat Canada in extra-time, and Japan seeing off a second-half onslaught against France.
There was good support for each team, but it was the USA fans who were celebrating in the eighth minute as Lloyd opened the scoring.
Tobin Heath got free down the left and crossed for Alex Morgan, whose heavy touch actually allowed her to chip up a ball that Lloyd arrived late to head home, stealing it off the toe of Abby Wambach.
It was the first time Japan had been behind all tournament and they responded superbly, going close twice in quick succession 10 minutes later.
A fine move ended with Nahomi Kawasumi's shot being blocked by Christie Rampone - although it may have been going wide - with Hope Solo thwarting Ogimion the rebound.
Solo then excelled herself, magnificently tipping Ogimi's header from Kawasumi's cross onto the crossbar, Ogimi smashing over the follow-up.
Heath was lucky to get away with handballing Aya Miyama's free-kick as Japan continued to dominate but they enjoyed a let-off themselves when Azusa Iwashimizu headed Amy LePeilbet's cross against her own post.
They should have equalised in the 33rd minute, Miyama the next to hit the woodwork after Shinobu Ohno was left alone in the box, the latter then sending a beautiful curling shot a few metres wide.
Both sides threatened early in the second half before Lloyd scored a stunning second goal in the 54th minute.
The Japan defence backed off as the midfielder carried the ball forward but even they could not have predicted the unstoppable 20-yard shot that flew into the net.
However, the world champions refused to buckle and, after bringing on Asuna Tanaka, they halved the deficit in the 63rd minute.
A lovely move saw Homare Sawa's shot blocked by Rampone and the ball broke for Ogimi to shoot home.
A sprawling Miho Fukumoto save prevented Rachel Buehler restoring the USA's two-goal lead while there was a desperate scramble at the other end after they failed to deal with a free-kick.
Lloyd was agonisingly close to a hat-trick when she hit a shot just over and Japan substitute Mana Iwabuchi should have equalised when she robbed Rampone 20 yards out but shot too close to Solo, who nevertheless produced a fine save.
Wambach could have netted late on but it did not matter that she missed out as the USA held on.
United States coach Pia Sundhage said: 'I painted a picture that we'd keep possession but Japan were too good for us.'
Of her players, she said: 'They found a way to win. Phenomenal, because that is not easy. They played with a huge heart and they changed the tactics and little bit. Wonderful.'