With his trademark sense of humour, Navalny took the extension of his jail time on new charges of embezzlement and contempt of court in stride, joking that his "space flight is being extended -- my ship has gotten caught in a time loop."
He also urged Russians to resist "these war criminals".
He stood trial inside his penal colony in the town of Pokrov outside Moscow.
"Navalny committed fraud -- the theft of property by an organised group," judge Margarita Kotova said, according to an AFP reporter present at the hearing.
The judge also found Navalny guilty of the less severe charge of contempt of court.
Navalny will serve his new sentence in a strict-regime penal colony, which will place him in much harsher conditions.
His lawyers, Olga Mikhailova and Vadim Kobzev, were detained by police following the verdict but were later freed.
Navalny's defence team said the new sentence replaces the one he is currently serving, meaning that he will not be freed for another eight years, instead of a year and a half.
'People are afraid'
Last year the opposition leader was sentenced to two and a half years for violating parole for old fraud charges while recovering from a poison attack with Novichok nerve agent that he blames on the Kremlin.
Navalny will also have to pay a fine of 1.2 million rubles ($11,500) and upon his release he will have to abide by various restrictions on his movement and activities for a further 1.5 years.
He appeared for Tuesday's hearing in the makeshift court wearing his black prison uniform, with journalists watching via a video link.
He listened closely as judge Kotova read out the verdict, sometimes smiling.
Navalny has denied the charges against him, saying they were punishment for challenging 69-year-old Putin.
Investigators accused Navalny of stealing for personal use several million dollars' worth of donations that were given to his political organisations.
The prosecutors had last week called for Navalny's sentence to be extended to 13 years as well as for his transfer to a strict-regime penal colony.
His wife Yulia Navalnaya said she was proud of her husband.
"The figure 9 means nothing whatsoever," she wrote on Instagram.
"I love you, my dearest person in the world, and I have not stopped being proud of you for many, many years."
Russia is seeing an unprecedented crackdown on dissenting voices, and AFP saw few Navalny supporters outside his penal colony on Tuesday.
"There are no people. Everyone's holed up in their apartments. They are afraid," supporter Leopold Banionis told journalists at the penal colony.
Many well-wishers said Navalny should remain strong and healthy, predicting he would not have to serve out his sentence in full.
"It is not possible to imagine that this will last nine years," one supporter, Asya Kazantseva, said on the politician's Facebook page.
'Predictable but shocking'
US State Department spokesman Ned Price condemned the verdict as a "sham ruling" and the "latest in a series of attempts to silence Navalny".
The EU's foreign policy chief Josep Borrell called for his "immediate and unconditional release".
Amnesty International's director for Eastern Europe and Central Asia, Marie Struthers, called the sentence predictable but "shocking."
"The world must not overlook this sentence and its significance amid the horrific human rights violations we have seen as a result of Russian aggression against Ukraine."
Navalny is Russia's main opposition leader and his team frequently publishes investigations into the wealth of Russia's elites that have garnered millions of views on YouTube.
Navalny's poisoning in 2020 with Novichok, a Soviet-designed military-grade nerve agent, and arrest on his return from rehabilitation in Germany last year sparked widespread condemnation abroad, as well as sanctions from Western capitals.
The Kremlin denied any involvement.
After his arrest, Navalny's political organisations across the country were declared "extremist" and shut down, while key aides have fled Russia.
Russia has also ramped up pressure on independent media and non-governmental organisations, declaring many "foreign agents", while others have stopped operating for fear of prosecution.
In an effort to further control the information available to its domestic audience amid Moscow's action in Ukraine, Russia this month restricted access to Twitter, Facebook and Instagram and a court banned Facebook and Instagram as "extremist" on Monday.