The Yamaha rider's 1m29.068s put him 0.390 seconds of second-placed Dani Pedrosa's Honda to finish an encouraging week on top.
Lorenzo's strong Phillip Island form came after a troubled Sepang test last week, in which he raged against the characteristics of the 2014 Bridgestone tyres, feeling that they favoured Honda.
The Spaniard also managed a race simulation on Wednesday, while both he and Yamaha team-mate Valentino Rossi - who was third on day three - tried a new fairing during the test.
Pedrosa attempted a race simulation but had to stop due to neck pain, which he put down to the recent intensive test schedule.
The Ducatis had issues too, with a front-end mechanical problem interrupting Cal Crutchlow's running and the illness that has hampered Andrea Dovizioso all week forcing him to park early.
Rain had been forecast for Wednesday, but ultimately only a brief shower intruded on proceedings.
There were two red flag stoppages, both for Moto2 rider Tito Rabat.
Although the Marc VDS man showed great pace during the week, he ended it with a destroyed Kalex after his second shunt of the day.
His team-mate Mika Kallio had also crashed heavily on Monday.
The works Yamaha, Honda and Ducati teams will not now run again until the season-opening Qatar Grand Prix on March 20-23.
The rest of the MotoGP field is testing at Losail from Friday to Sunday this week.