The American quartet of Aaron Peirsol, Eric Shanteau, Phelps and David Walters broke the old standard of 3:30.68 set by the United States in winning Olympic gold in Beijing.
Germany finished second in 3:28.58 with Australia third in 3:28.64.
Big day for Phelps' teammate Ryan Lochte too, as he completed the individual medley double by winning the men's 400m that gave him the fourth gold.
Lochte clocked four minutes 07.01 seconds, beating his teammate Tyler Clary and Laszlo Cseh of Hungary.
Britain's Liam Tancock bettered his own world record to win the men's 50m backstroke final.
Tancock clocked 24.04 seconds with Japan's Junya Koga finishing second and South Africa's Gerhard Zandberg third.
Russia's Yuliya Efimova won the women's 50m breaststroke title in a world record time of 30.09 seconds, shattering the previous mark of 30.23 set by Canadian Amanda Reason on July 8 in Montreal.
Germany's Britta Steffen claimed the 50m freestyle gold in 23.73 seconds.
Steffen broke the previous world record of 23.96 set by Marleen Veldhuis of the Netherlands in Amsterdam on April 19.
Olympic champion Oussama Mellouli of Tunisia won the men's 1,500 meters freestyle with a clocking of 14 minutes 37.28.
Canada's Ryan Cochrane finished second and China's Sun Yang was third.
Hungarian Katinka Hosszu triumphed in the women's 400m individual medley final in four minutes 30.31 seconds, beating Zimbabwe's Kirsty Coventry and Olympic champion Stephanie Rice.
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