Phelps moved alongside Larisa Latynina on 18 medals following the 200m Butterfly, although any sense of achievement may have been bittersweet given he was beaten at the touch by South African Chad le Clos and had to settle for silver.
The 27-year-old then anchored the United States 4 x 200m Freestyle Relay team to gold as he moved on to 19 medals - with Phelps now the owner of 15 gold, two silver and two bronze medals.
The Baltimore swimmer still has three races to come and is expected to finish his Olympic career with 22 medals.
The Bob Bowman-trained athlete paid tribute to his three relay team-mates, and said: 'I thanked those guys (in the huddle) for helping get to this moment.
I thanked those guys (in the huddle) for helping get to this moment.Michael Phelps
'I told those guys I wanted a big lead in the last leg and they gave it to me.
'I just wanted to hold on, I just wanted to thank them for allowing me to have this moment.'
Phelps had the Butterfly won until the final metres but he got his finish wrong - his usual perfect spotting of the wall replaced with a glide that would have had Bowman tearing his hair out.
Phelps was disappointed but was philosophical, saying: 'Obviously I would have liked to have had a better outcome in the 200m fly.
'Chad swum a great race, I have got to know him over the last year, he is a hard worker, a fast racer and a tough competitor.
'I would have liked to have won my last race, but it wasn't a terrible time. It was decent.'
Le Clos was hugely emotional, crying on the podium, seemingly stunned by the magnitude of his achievement which saw the South African beat his idol by 0.05 seconds in 1:52.96.
He said: 'This is a dream of mine, I have always said Michael Phelps was my hero.
'I wanted to be in the final for my main event, I achieved that goal and my coach said you have done all you have to do.
'But I just remember sitting in the call room thinking that Michael Phelps has never lost this race for 10 years in international meets.
'I remember turning in the last 50 and just looking at him underwater and realising this is my hero, it's crazy.
'I can't describe how I felt. In the last 25 metres, I can't explain what came over me.'
'I'll have to try and defend my title in four years time, but to beat Michael Phelps is something I have wanted my whole life, it is exactly what I have been dreaming off since I was 12.'
Meanwhile, Ye followed up her victory in the 400m Individual Medley, with the 16-year-old adding the shorter Medley title.
Tonight she turned third after 150m before producing a blistering freestyle leg to win in a new Olympic record of 2:07.5.
Australian world champion James Magnussen was quickest into the 100m Freestyle final.