Cielo, who set a world record in the 100 freestyle on Thursday, won the 50 in a time of 21.08 seconds on Saturday while Bousqet was runnerup in 21.21.
Coventry swam a time of 2:04.81, well under her previous record of 2:05.24. It was her third career gold medal in the FINA World Championships.
Auburn swimmers have won 10 medals at the 2009 World Championships in Rome. If Auburn was a country, it would be third in medal count behind the USA's 18 and Australia's 12.
"Today was a great day for Auburn swimming," Auburn head coach Brett Hawke said. "We wanted to come to Rome and show the world what Auburn is all about. Cesar and Fred have proved themselves to be the top sprinters in the world right now.
"We came here to win medals," Hawke added. "That is what we're doing. Auburn is doing better that most countries here. I think we've really made a statement here in Rome. I'm so proud of all our swimmers and everything we've achieved here."
A third Auburn swimmer, George Bovell, finished third in the 50 with a time of 21.51. Bovell, Cielo and Bousquet train in Auburn under Hawke's direction.
Tyler McGill, who will be a senior at Auburn this coming season, was seventh in the men's 100 butterfly in 51.42.