Sykes and team-mate Loris Baz ran without transponders on their bikes - and the team said the Briton set a mark of 1:40.5.
Italian Melandri managed 1:40.758, with Davide Guigliano second and Eugene Laverty third on Aprilias.
"We have to be very happy after this test. We learned some things yesterday [in the wet] and also today in dry track conditions," said Sykes.
"We were able to test very constructively."
Melandri reflected: "Today was very positive and I think we are well prepared for Phillip Island. We tested a lot of things, for example regarding electronics and got a clear understanding which direction we have to take.
"Of course, there is still work to do but especially with the chassis and the electronics we made a good step."
Northern Irishman Laverty suffered low-speed crash which he played down later.
"The crash was due to a loss of grip when I tried pushing beyond the track grip limit, but it didn't compromise our testing sessions," he said.
Pata Honda riders Leon Haslam and Jonathan Rea were frustrated by electronic glitches in the new software systems designed by Honda's MotoGP project team.
"Some things just can’t be fixed on site and the electronics problem we had was one of those. The system was taking too much power away so we really needed more track time to sort that out," said Rea.
1 Marco Melandri Goldbet BMW 1'40.758
2 Davide Guigliano Althea Aprilia 1'40.861
3 Eugene Laverty Aprilia 1'41.044
4 Leon Camier Fixi Suzuki 1'41.184
5 Jonathan Rea Pata Honda 1'41.641
6 Sylvain Guintoli Aprilia 1'41.683
7 Chaz Davies Goldbet BMW 1'41.726
8 Leon Haslam Pata Honda 1'42.411
9 Jules Cluzel Fixi Suzuki 1'42.632