The test had originally been scheduled to follow the third round of the season at Estoril, but was cancelled due to bad weather and rescheduled to follow the two-day test immediately after the Catalunya Grand Prix.
Honda had already declared it only wanted to trial Bridgestone's new compound during testing. The team was able to do sufficiently at Barcelona, and therefore elected to skip the Aragon test.
Yamaha dominated as a result, locking out the top four positions - the two works bikes ahead of the satellite Tech 3 entries.
Lorenzo, again trialling new engine specifications and electronics, went fastest late on with a 1m49.187s.
“This test has been very important because it’s not easy to find the best set up for the 1000cc bike here as there is so much change from the 800," he said.
"We tried the engine again like we did in Barcelona, there wasn’t so much difference so the engineers now have to make a decision for moving forward. They will consider the data from today to help them.”
That put him just over a quarter of a second clear of Spies, and exactly half a second ahead of Tech 3's Cal Crutchlow.
“Today was a good test, to come back after not such a fantastic race on Sunday and be consistently fast here and in the Catalunya test is important," said Spies. "We’ve worked really well with the bike and the electronics and just tried to change a few things and fine tune.
"The track was a lot better than we thought, we were expecting it to be quite dirty but it wasn’t. I feel like I’m getting back up to the potential of the bike and myself which is good.”
Briton Crutchlow enjoyed a successful test, trialling components he was not able to following his high-speed crash at Catalunya and ending the day 0.2s clear of Tech 3 team-mate Andrea Dovizioso.
Hector Barbera (Pramac Ducati) was the fastest non-Yamaha rider in fifth, having spent the day evaluating new electronics.
Works riders Nicky Hayden and Valentino Rossi finished sixth and eighth respectively, split by the fastest Honda, the Gresini of Alvaro Bautista.
As expected neither Hayden nor Rossi tested Ducati's new aluminium swingarm, which Rossi dropped halfway through the Catalunya Grand Prix weekend.
LCR Honda's Stefan Bradl and the Cardion Ducati of Karel Abraham rounded out the top 10 ahead of the lead CRT of Michele Pirro (Gresini).
Avintia and Forward were the only other CRT teams to attend. Forward's Colin Edwards ended 13th fastest, splitting Yonny Hernandez (12th) and Ivan Silva (14th), the latter of whom damaged the part-carbon Inmotec chassis he was testing with a crash.
Pos Rider Bike Time Laps
1. Jorge Lorenzo Yamaha 1m49.187s 59
2. Ben Spies Yamaha 1m49.442s + 0.255 57
3. Cal Crutchlow Yamaha Tech 3 1m49.687s + 0.500 67
4. Andrea Dovizioso Yamaha Tech 3 1m49.887s + 0.700 54
5. Hector Barbera Pramac Racing 1m50.196s + 1.009 64
6. Nicky Hayden Ducati 1m50.204s + 1.017 66
7. Alvaro Bautista Honda Gresini 1m50.294s + 1.107 56
8. Valentino Rossi Ducati 1m50.369s + 1.182 78
9. Stefan Bradl LCR Honda 1m51.146s + 1.959 72
10. Karel Abraham AB Motoracing 1m51.977s + 2.790 19
11. Michele Pirro Honda Gresini 1m52.452s + 3.265 51
12. Yonny Hernandez Avintia Racing 1m52.502s + 3.315 64
13. Colin Edwards Forward Racing 1m52.589s + 3.402 53
14. Ivan Silva Avintia Racing 1m53.929s + 4.742 69