The 23-year-old Frenchman, who finished as runner-up in last year's Atlantic Series, was running with Conquest Racing for the third day in a row.
And his lap of 49.806 seconds, easily the best set by anybody all week at the Florida track, showed that his team have come a long way since their abysmal run at the start of last year.
"I think we did a good job," Perera said. "It was a crescendo - each session we were faster and we tested many things for all the phases of a race weekend and we did well in each. So, it's good that we can already fight with the top guys."
Perera ends Sebring test on top
Perera was just 0.044 seconds quicker than American Graham Rahal, who out-paced his new Newman/Haas/Lanigan team-mate Justin Wilson for the first time all week.
Third quickest was series veteran Alex Tagliani for PKV - one place ahead of Oriol Servia - who has already signed for the team for the coming season.
"I'm very, very happy and very impressed with the team," Servia said. "We did the last race in Mexico and we obviously had a good car. They have been working hard all winter and all the new things they did, they were better. So I'm really happy.
"The conditions today were nothing like you are going to find this season so we didn't really want to focus too much on the set-up. We just wanted to test and try things and that's what we did. It was also good to have Alex here to compare notes."
British star Wilson, the championship runner-up for the past two seasons, was fifth.
"I'm very pleased with the way the test has gone," said Wilson, who ran 269 laps during the test. "The team has worked hard to make me comfortable in the car and it feels good.
"I'm not sure how relevant the results of this test in Sebring will be but we learned some things to build on.
"We did well here and stayed disciplined and hopefully learned some things that will help us be competitive this season. I'm looking forward to building on our program at the next test at Laguna Seca."
Surprisingly down in sixth was Franck Montagny. The pace-setter on the first two days of the test was the only man not to improve his time on the final day, but he still looks to have done enough to secure a drive with Forsythe Pettit for the season.
Dale Coyne's Bruno Junqueira, Pacific Coast's Alex Figge, Conquest's Simon Pagenaud and Rocketsports' series newcomer Enrique Bernoldi completed the top ten.
Conquest to double ChampCar assault
Conquest to run two cars this year