Putin, who was then prime minister, ordered seven of the country's largest oil and energy companies to pump more than $12 million into the club's coffers.
The cash injection helped turn Tom's fortunes around both on and off the pitch, allowing the club to pay off most of its debt and also boosting the team's morale.
Tom, who owed nearly 600 million roubles in back pay to their players and staff in 2009, had needed around 400 million roubles to keep the club afloat.
However, Putin warned former Tom bosses that it was a one-off deal and they should not expect any such help in the future.
"Many clubs have had to deal with such problems, not just in Russia but worldwide," Sergei Zhvachkin, who became the club's new president in March soon after Putin appointed him governor of the Tomsk region, told Reuters.
"Look at Chelsea. They too were on the verge of bankruptcy just a decade ago, before Roman Abramovich came to rescue them."
Russian billionaire Abramovich has invested hundreds of millions of pounds of his own money into Chelsea since buying the west London club for some £17 million in 2003.
"Now they're among the biggest clubs in Europe," Zhvachkin said. "It just shows that nothing is impossible in football."
Tom has continued to face problems both on and off the field.
Their experienced coach Valery Nepomniashchy, who led Cameroon to the 1990 World Cup quarter-finals and has worked with national teams in China and Uzbekistan, quit last year and the team were relegated to Division One (second tier league) in May.
Last month, the club was fined 30,000 roubles by local authorities for failing to pay wages to its staff on time.
In addition, local prosecutors have opened a criminal case against their former general director Yuri Stepanov, charging him with embezzlement linked to the 2006 transfer of Russia international Pavel Pogrebnyak.
Investigators said a third party had been paid $400,000 to obtain Pogrebnyak's transfer from Spartak Moscow to Tom.
The following year, the well-travelled striker moved to Zenit St Petersburg, then to Bundesliga's Stuttgart before joining London club Fulham last season. He now plays for their English Premier League rivals Reading.
Stepanov has also left the club and the criminal case was closed earlier this year.
Following a summit meeting in the Kremlin headed by Putin this year, Rosneft and Gazprom - the country's largest oil and energy companies respectively - agreed to share the cost of running the club along with the regional government.
Tom are currently undergoing restructuring after Gazprom and Rosneft officially became the club's joint owners along with the Tomsk region.
"I think it's only fair for the state companies, such as Gazprom and Rosneft, to give something back to the people of our region for using our natural resources," said Zhvachkin.
"With the help of Gazprom and Rosneft we have been able to pay off some 450 million roubles of the money owed to former players and staff but still owe about 150 million in back wages," added deputy governor Chingis Akatayev.
The team are looking for a quick return to Russia's top flight next year after comfortably leading Division One midway through this season's campaign.
They have a good mix of experienced players, such as former Scotland striker Garry O'Connor, as well as young blood, including Pogrebnyak's younger brother, 20-year-old Kirill.
"We have good crowds at almost all our home games even when the temperature drops well below zero, especially when we face (arch-rivals) Sibir Novosibirsk. It's our Siberian derby," said long-time Tom fan Sergei Simonov.
The club, however, has still been criticised for relying heavily on government subsidy rather than trying to work out a solid economic plan.
Zhvachkin said he would welcome a private owner with open arms but added it was nearly impossible to find a local tycoon who was willing to risk his own money by investing in the struggling club.
"Well, I can ask Abramovich to sell Chelsea and put his money into our club but I don't think he would accept such an offer," he added with a smile.
Despite the recent problems, Zhvachkin dreams of one day playing in the Champions League.
"Who knows, maybe I'll live to see the day when Tom will host a top club, like Chelsea, in a European Cup match," he said looking up and rolling his eyes.
- Sports & Recreation