The sentence, imposed by top anti-corruption judge Sergio Moro in Curitiba, was a landmark for the country's battle against rampant, high-level graft.
Moro, frequently cited as a hero by Brazilians at demonstrations, cited Cunha's conviction for corruption, money laundering and tax evasion in handing down the sentence of 15 years and four months.
Cunha "took wrongful advantage of his mandate as a federal (congressional) deputy," Moro wrote. "There can be no more serious offense than betraying the parliamentary mandate and the sacred trust placed in him by the people for personal gain."
Cunha's defense lawyer said an appeal would be lodged. However, Cunha will remain incarcerated in Curitiba, in the south of Brazil.
Prosecutors said he took millions of dollars in bribes as part of a sprawling corruption network in which politicians and major contractors embezzled from state oil company Petrobras.
The investigation, dubbed Operation Car Wash, has upended Brazilian politics, with dozens of politicians accused of participating in the scheme.
A member of current President Michel Temer's PMDB party, Cunha, 58, was one of Brazil's most influential politicians until he was removed from his speaker's post in July and arrested in October 2016.
When he outmaneuvered Rousseff and triggered impeachment proceedings, she was replaced by Temer -- who at the time was her conservative vice president in a coalition between the PMDB and Rousseff's Workers' Party. This briefly left Cunha first in the line of succession for the presidency.
Widely hated by Brazilians, Cunha earned a reputation as the ultimate master of dark political arts and was dubbed Brazil's Frank Underwood -- the scheming, corrupt anti-hero of the hit Netflix series "House of Cards" about a US politician.
Symbol of rot
Cunha is only one of many politicians tainted by the Car Wash probe or by other investigations. No less than one in three members of the lower house -- 155 out of 513 deputies -- face criminal cases, according to the specialist political website Congresso em Foco.
That number could spike soon when the Supreme Court, which handles all cases involving sitting politicians, acts on a request by the prosecutor general to open new Car Wash-related probes against about 100 as-yet unnamed politicians.
Among the many big names already in the crosshairs is former president Luiz Inacio Lula da Silva, a larger-than-life figure in leftwing Latin American politics who founded the Workers' Party and helped Rousseff into power.
Like Cunha, Lula is accused of corruption and money laundering and will be tried by Moro because he is no longer a serving politician.
By contrast, the overburdened Supreme Court may not complete cases of many other high-profile suspects for years -- raising the question of whether Cunha is the sign of more to come from Car Wash or one of its high water marks.
Cunha stood out in Congress as a feared and grudgingly admired political operator who ended up symbolizing the thieving and lack of accountability in the capital Brasilia.
Even before his arrest, Cunha was already in trouble for lying to Congress. Through a variety of delaying tactics he managed to avoid his eventual expulsion from the legislature for months.
During his trial before Moro he asked Temer to be a witness, but his questions were excluded after being ruled to be an attempt to "intimidate" the president even from behind bars.
Cunha's sentence is one of the harshest so far in the Car Wash saga.
Marcelo Odebrecht -- former CEO of the Odebrecht construction giant, which was integral to the Petrobras embezzlement-and-bribery scheme -- was sentenced to 19 years and four months, while Lula's former chief of staff Jose Dirceu was sentenced to 20 years and 10 months.