The Movistar Yamaha rider made up for his disappointing performance on the first day to move from 0.881s to 0.370s off the pace set by reigning MotoGP champion Marc Marquez.
"Sincerely I'm a lot more satisfied about today because at the end my minimum target was to stay in the top ten [to go straight through to Qualifying 2 on Saturday] and this practice already is unbelievable because there are ten bikes in three tenths!" Rossi said after his second practice run. "So I'm not happy about my position but I'm not far from 'pole'."
However, Rossi was once again unhappy with the rear tyre of his bike as he felt it did not grip the track very well.
The 36-year-old added that he is unsure about whether to use a soft or hard tyre for the race. As a result of this, he will use Saturday's qualifying run to figure out which tyre is best suited to the Losail International Circuit.
"It will be very hard tomorrow in qualifying but we improved the bike, the setting and my pace is not so bad," he said. "Very similar to the other top guys.
"We have to work a lot on the rear because maybe we can use the soft or the hard. So tomorrow will be important to understand which tyre to use for the race. At the moment it is 50/50."