The reigning four-time champion was fourth fastest overall on his Kawasaki ZX-10RR as series rookie and 2006 125 Grand Prix champion Alvaro Bautista topped the times overall.
Riding the much-hyped new Ducati V4 R for the Aruba.it Racing Team, Spaniard Bautista posted a time of 1m 30.303s, which put him four-tenths-of-a-second clear of Rea.
Tom Sykes, who has been highly impressive at Phillip Island so far on the factory BMW S1000RR, was two-tenths down on Bautista as the Yorkshireman slotted into second place.
However, the opening races this weekend are when it really matters and Ulsterman Rea will be hoping to close the deficit to Bautista and put some solid early points on the board.
Tuesday's final test day was interrupted by a series of red flags in the morning session, thwarting riders’ plans to undertake a race simulation, but Rea was satisfied overall with the progress he made.
“This has been a really positive test and we have been able to analyse a lot of items and change things in the bike to see exactly what the track requires,” he said.
“This track is so unique because of the energy and load we put into the rear tyre, because of those fourth and fifth gear corners. Now we have a lot of data but unfortunately today there were a lot of red flags and we were not able to complete a long run or maximise a time attack.
“So this has been a huge data gathering two-day test and it will prove very valuable for race weekend,” he added.
“With three races this year we need to be clever with the timetable and Sunday will be very a tight day for many reasons: the racing itself, trying to take on board food and - being in a factory team - the media commitments, so Sunday will be busy.
“From a racing point of view, I am quite happy.”
Rea’s team-mate, Leon Haslam, was third fastest but only 0.054s ahead of Rea, with Marco Melandri (GRT Yamaha) and Toprak Razgatliogu (Turkish Puccetti Racing Kawasaki) next as half-a-second covered the top-six.
Eugene Laverty was 16th fastest on the Go Eleven Ducati V4 R as he continues to find his way with the new bike.
Free practice will get under way at Phillip Island on Friday.