After two winless seasons with Ducati, the Italian has rejoined the Japanese squad at which he spent seven years, winning four premier class titles and 46 grands prix along the way.
Early morning rain ruined any hopes of Rossi setting competitive times however, while cold afternoon conditions effectively truncated the day's running.
With the aim of giving Rossi maximum seat time on the 2013 M1, Yamaha will now travel overnight to Aragon in order to join Wednesday's World Superbike test.
Rossi did at least complete 28 laps for his new squad, although having missed the early window of dry running he was more than seven seconds slower than overall pacesetter Alvaro Bautista.
Both Nicky Hayden and Andrea Dovizioso, the man who replaced Rossi at Ducati, managed to go faster. Rossi boasted better long-run pace, however.
Dovizioso ended the day third fastest and Hayden fifth, the pair split by Hiroshi Aoyama on the Avintia Blusens bike on which he will compete next season.
Other newcomers did not even manage to go out, with Moto2 champion Marc Marquez (Honda) and fellow graduate Bradley Smith (Tech 3) opting not to run at all.
Their new team-mates Cal Crutchlow and Dani Pedrosa followed suit, as did 2012 MotoGP champion Jorge Lorenzo.
Andrea Iannone, newly installed in Ducati's restructured satellite Pramac team, was late to join the circuit but ended the day with 40 laps under his belt, behind only Dovizioso and Hector Barbera on the second Avintia machine.
1 BAUTISTA, Alvaro Go & Fun Honda Gresini 1:35.936
2 BRADL, Stefan LCR Honda MotoGP 1:36.198
3 DOVIZIOSO, Andrea Ducati Team 1:39.868
4 AOYAMA, Hiroshi Avintia Blusens 1:42.239
5 HAYDEN, Nicky Ducati Team 1:42.571
6 ROSSI, Valentino Yamaha Factory Racing 1:43.736
7 PIRRO, Michele Pramac Racing Team 1:44.297
8 CORTI, Claudio NGM Mobile Forward Racing 1:45.814
9 DE PUNIET, Randy Power Electronics Aspar 1:46.045
10 ESPARGARO, Aleix Power Electronics Aspar 1:46.060
11 EDWARDS, Colin NGM Mobile Forward Racing 1:46.426
12 ABRAHAM, Karel Cardion AB Motoracing 1:46.992
13 IANNONE, Andrea Pramac Racing Team 1:47.772
14 BARBERA, Hector Avintia Blusens 1:49.457
- PETRUCCI, Danilo Came IodaRacing Project
- PEDROSA, Dani Repsol Honda Team
- CRUTCHLOW, Cal Monster Yamaha Tech 3
- SMITH, Bradley Monster Yamaha Tech 3
- BYRNE, Shane Paul Bird Motorsport
- MARQUEZ, Marc Repsol Honda Team
- LORENZO, Jorge Yamaha Factory Racing