The 16-year-old followed up her incredible win in the 400 medley three days earlier with another impressive display of power and perfect technique.
But this time she had to work much harder. She was third when they turned for home but overhauled her rivals to win the multi-discipline event in two minutes, 07.57 seconds.
Coutts, who won a relay gold for Australia on Saturday took second place, just ahead of America's Caitlin Leverenz.
Stephanie Rice, the gold medallist in Beijing four years ago was fourth while world record holder Ariana Kukors was fifth.
Ye won the Asian championship as a 14-year-old in 2010 then added the world title last year but her performances in London, where millions of people around the world are seeing her compete for their first time, have triggered thinly-veiled accusations of doping by the Chinese.
Ye has denied any wrongdoing and Olympic officials hinted her test results from the 400 came up clean.
"We would only comment if we had any adverse finding," IOC spokesman Mark Adams said earlier. "I am not commenting, so you can draw your own conclusions."
Miley finished in a time of 2:11.29 minutes but the 22-year-old believes that while she has some sympathy for Shiwen, amidst doping allegations, she says it’s not her job to worry about it.
“It is a shame, but as swimmer as we don’t tend to get involved – we just get in and race and that’s our job,” said Miley.
“When she raced, she put in an outstanding performance and you can’t but applaud that. It’s a shame that people start analysing that that these queries come up.
“For us, it’s not something that we shouldn’t be worry about, but something the officials and the governing body do.
“At the end of the day, it’s ahead-to-head race and she did an amazing race and made us swim faster.
“I’m so happy that I was able to make a final, when last time I was 11th – now I’m seventh in the world. I can’t knock that so I’m really happy,
“This meet was so much better than Beijing. The atmosphere has been great – I know I keep saying it but it really is.
“As a swimmer, I’ve really loved every moment of it – it’s wonderful. I’m looking to having a break, physically and mentally, and then we’ll discuss how to move forward.”