The Italian, who finished 10th last year, set the best time of 1:50.301.
The BMW of Marco Melandri was over four tenths further back with Sylvain Guintoli, on the works RSV4, in third.
Kawasaki's Tom Sykes and Loris Baz were also testing but elected to ride without transponders so no times were available.
Poor weather last weekend in Spain saw Alstare Ducati's Carlos Checa and Ayrton Badovini muster under three hours' track time on their new Panigale 1199R machines.
Times:
1 Davide Guigliano (Althea Aprilia) 1'50.531
2 Marco Melandri (BMW) 1'50.950
3 Sylvain Guintoli (Aprilia) 1'52.909
4 Leon Camier Fixi (Suzuki) 1'53.285
5 Eugene Laverty (Aprilia) 1'53.410
6 Chaz Davies (BMW) 1'54.084
7 Jules Cluzel (Fixi Suzuki) 1'54.168
8 Leon Haslam (Pata Honda) 1'54.548
9 Jonathan Rea (Pata Honda) 1'54.907
