The 30-year-old, who has now won seven world championships in the premier 500cc/MotoGP class, had taken the 2009 title lead with his first win of the season at round three in Jerez.
Fiat Yamaha team-mate Jorge Lorenzo and Ducati's Casey Stoner then fought back, and all three were level at the top of world championship standings after round six in Catalunya.
The next five rounds proved crucial, with Stoner falling victim to mystery fatigue problems while Lorenzo crashed out at both Donington Park and Brno.
Rossi won three of those five races to build his title lead to a peak of 50 points after the Czech Republic, but instantly lost half that advantage - and threw Lorenzo a championship lifeline - when he crashed out of the following Indianapolis Grand Prix.
The see-saw continued with a Rossi victory at Misano and then a Lorenzo win at Estoril - when Rossi was only fourth, dropping his title advantage to 18 points.
The pressure was on for Phillip Island but Lorenzo cracked first, making a mistake into turn one and crashing out, effectively wrecking his hopes of taking the title down to the final round in Valencia.
38 points clear heading into Sepang, Rossi only needed to be 25 points ahead of Lorenzo to wrap up the title - a feat he easily achieved after converting a record 58th pole into third place in the rain-delayed race, one place in front of Lorenzo.
“Nine world championships is a great achievement, I'm so happy!” said Rossi. “I would need one hour to thank everyone! Starting with everyone at Yamaha - Furusawa-san, Lin Jarvis, Davide Brivio and all my guys, especially Jeremy. I couldn't have done it without Jeremy and he is like my motorcycle father!
“I also have to thank my family and friends - Stefania, Graziano, Uccio, Albi...so many! All the team, Yamaha and Bridgestone; together we've done a great, great job and it's always a huge enjoyment to ride and work with these people.
“In order to stay at this level through a whole season you have to be calm and have the right people around you and this is what I have. We've stayed concentrated and focused even in the bad moments, so we can congratulate ourselves with this ninth title.”
Rossi suffered a scare at the start of the race when he ran wide whilst trying to outbrake Dani Pedrosa into turn one and had plummeted to tenth - behind Lorenzo, who had started from the back of the grid – by the end of a soaking first lap.
The #46 then shadowed his team-mate up the order, before taking fourth from the young Spaniard on lap eight of 21. That became third position when Andrea Dovizioso crashed out on lap 15, allowing Rossi to reach his target of celebrating championship victory from the podium.
"Without the rain it could have been a brilliant race, with the four top riders fighting together, but the rain changed it," said Rossi of the weather. "It was scary for everyone because all the work we'd done was useless and we were riding 'blind' with the setting.




