Rossi finished first in the championship with 306 points, 72 points ahead of second-place Jorge Lorenzo. Six wins was the lowest number of wins Rossi has had in a championship winning season; the previous minima were nine in 1999 in the 250cc class and 2003, 2004 and 2008 in MotoGP. Rossi also failed to win at Mugello for the first time since 2001. Rossi and RCV triumphant at Suzuka". Crash.net. Crash Media Group. 7 April 2002. Archived from the original on 16 July 2015 . Retrieved 15 July 2015.

Rossi finished third in the championship with 198 points, 123 points behind champion Marc Márquez. This was Rossi's first winless season since 2012 when he raced with Ducati and his first ever winless season with the Factory Yamaha team.Rossi triumphs in all-Italian showdown". Crash. 8 June 2003. Archived from the original on 16 August 2019 . Retrieved 16 August 2019. In Australia Rossi took his second victory of the year. He benefitted from an accident of Marc Márquez who had been leading the race. It was Rossi's sixth win at the circuit after five consecutive wins he took from 2001 to 2005. [294] In Malaysia, another second-place finish followed when he initially took the lead halfway in the race after passing Lorenzo. Márquez passed both Lorenzo and Rossi, pulling a gap and finishing 2.445 seconds ahead of the Italian. [295] Rossi took his first pole position since the 2010 French Grand Prix at the Valencian Community race, his 60th pole position in Grand Prix racing. [296] He finished in second place behind Márquez in the race. [297]

When Rossi wanted to shake Stoner's hand in the parc fermé, he angrily refused. At the press conference, Stoner claimed that some of Rossi's moves were considered "aggressive" but Rossi called it "just racing". [446] After this, Casey Stoner made the comment "I have lost respect for one of the greatest riders in history." [447] For the comment, Stoner apologised to Rossi at the next race. [448]In 2009, Rossi and Lorenzo resumed hostilities with Rossi emerging as champion again. Over the course of the season, Rossi defeated Lorenzo in several tight battles – such as Assen, Sachsenring, Valencia and, most memorably, Lorenzo's home race in Catalunya. Both were battling hard on the Catalan circuit, with Lorenzo taking the lead on the final lap. Rossi tried to overtake him in the usual spots but failed, with many assuming Lorenzo was going to win the race. However, Rossi managed to pass him going into the final corner, where many assumed overtaking was impossible, to take an unlikely victory.