State news channel Vesti-24 showed footage of the suspects being searched. They were lying face down on the ground as FSB officers found a grenade and a lump of what looked like plastic explosives.
Matviyenko, a former diplomat who helped Putin cement Kremlin control over the northern city where was born, appeared on state television to thank the security services.
"The law enforcement agencies have worked very professionally, as you can see," she said.
"You just cannot rule out any terrorist acts against politicians and employees of the state to undermine the situation and attract attention."
She said she had no plans to increase her own security because of the threat.
Elected governor of St Petersburg in 2003, Matviyenko had a second, five-year term approved by Putin in December.
Kremlin supporters have warned that extremist groups and radicals financed from abroad could try to undermine political stability in the country ahead of elections.
Critics have suggested that reports of "plots" against senior figures are released by the government for poitical ends.