Lorenzo was pushed hard by Nicky Hayden, with the Ducati rider less than a tenth of a second slower than the Spaniard.
It was a good day for Suzuki, who gave their GSV-R1000 its first public airing as Randy De Puniet was only three-quarters of a second off the pace, lapping in a time of 1:42.676.
Lorenzo was slower than his pole time from Saturday at the Spanish track, but it was not clear what new parts were being evaluated.
Meanwhile, Suzuki bosses have said they will not enter MotoGP until 2015 as they further develop their bike.
MotoGP Catalunya test times: 1 LORENZO, Jorge Yamaha Factory Racing Team - 1:41.908
2 HAYDEN, Nicky Ducati Team - 1:41.955
3 BRADL, Stefan LCR Honda MotoGP - 1:42.227
4 DOVIZIOSO, Andrea Ducati Team - 1:42.417
5 CRUTCHLOW, Cal Monster Yamaha Tech 3 - 1:42.462
6 ROSSI, Valentino Yamaha Factory Racing Team - 1:42.513
7 ESPARGARO, Aleix Power Electronics Aspar - 1:42.537
8 DE PUNIET, Randy Suzuki Test Team - 1:42.676
9 IANNONE, Andrea Energy T.I. Pramac Racing Team - 1:42.697
10 SMITH, Bradley Monster Yamaha Tech 3 - 1:43.180