Rossi put in 39 laps with a best time of 1min 39.525sec with reigning world champion Lorenzo, who was fastest Saturday, just 0.015sec behind.
Yamaha Tech3's Cal Crutchlow filled out the top three.
"Today's test session was very positive for us. I'm so happy, especially because we used a different style of setting," said Rossi.
"It is very important for us to understand this setting, which can help and effect my riding style to ride the bike in a better way and stay more constant, especially with good lap times on old tyres.
"To make the first position with a time of 39.5 is good and also being as fast as Jorge."
Lorenzo complained that the wet-dry conditions in Jerez made handling difficult.
"The track was dry but not in perfect condition. There was not so much grip and we had some problems in some corners, where the bike was not very stable,"
"The track is not in the best condition, it's dry but it's not perfect because of the rain. I think we have to focus on getting more stability on acceleration and get more comfortable with the race pace."
The third and final day of testing is on Monday with the 2013 season getting underway in Qatar on April 13.
1. Valentino Rossi (ITA/Yamaha) 1:39.525,
2. Jorge Lorenzo (ESP/Yamaha) at 0.015,
3. Cal Crutchlow (GBR/Yamaha Tech3) 0.049,
4. Dani Pedrosa (ESP/Honda) 0.105,
5. Andrea Dovizioso (ITA/Ducati) 0.797,
6. Alvaro Bautista (ESP/Honda Gresini) 1.161,
7. Marc Marquez (ESP/Honda) 1.189,
8. Stefan Bradl (GER/Honda LCR) 1.258,
9. Andrea Iannone (ITA/Ducati Pramac) 1.563,
10. Nicky Hayden (USA/Ducati) 1.800