In today's heats, the pair were alongside each other as Cavic made a storming start and Phelps appeared to be out of touch.
Last at the turn, the USA swimmer then produced his customary storming second 50m to overtake Cavic and touch first in 51.72, second overall behind his conqueror in the 200m Butterfly, Chad le Clos, who clocked 51.54.
I knew today was going to be a fast one, this is my last prelim swim ever, so it was fun to be able to do a fast timeMichael Phelps
Phelps said: 'We have had some pretty closes races in our day. Someone tweeted this morning we were next to each other, in the morning swims I haven't been able to catch a break.
'I knew today was going to be a fast one, this is my last prelim swim ever, so it was fun to be able to do a fast time.'
The 27-year-old also described the moment he received a phone call from USA president Barack Obama yesterday.
'He just got on and was saying how everyone is supporting me and is behind me at home and how proud everyone is of me. That was pretty cool.
'And he finished by saying, "Make sure you tell your mom I said hi" - it was a good call.'
Great Britain's Rebecca Adlington swam the fifth fastest time in the world this year as she qualified quickest for the women's 800m Freestyle final in 8:21.78.
George Bovell of Trinidad heads the men's 50m Freestyle heats, while Missy Franklin's 2:07.54 leads the women's 200m Backstroke.