A total of 745 were convicted in that period.
The European Union has been pressing Turkey to abolish or overhaul the law as part of Turkey's campaign for EU membership.
The opposition, resentful of what it calls EU interference in Turkey's affairs, wants the law to remain intact.
Prior to the debate, Devlet Bahceli, who heads the Nationalist Action party, said: "I am making this call for the last time, come back from the brink of making a mistake. Do not pave the way for insults to Turkish values."
Bahceli also called for a referendum to allow the people to decide "whether they want or don't want Turkish values and Turkey's honorable history to be insulted".
The government of Recep Tayyip Erdogan, Turkey's prime minister, has been criticised for slow progress on changes to Article 301 and other EU-backed reforms.
Critics say that Erdogan, whose Islamic-rooted party is facing possible closure for allegedly violating the country's secular principles, is now keen to be seen to be advancing Turkey's EU bid.
Opponents of Article 301, meanwhile, say the government-proposed changes are only cosmetic and will have little impact on Turkey's EU bid.
They also say there are other freedom-curbing laws in Turkey's penal code that need to be changed, including Turkey's anti-terror law and laws on crimes against the national founder, Mustafa Kemal Ataturk.
Under Article 301, the maximum sentence for denigrating Turkish identity or insulting the country's institutions is three years in prison.
The government proposal would reduce the time to two years, and grant a possible suspension of the sentence for first-time offenders.
Under the plan, prosecutors would need to seek the justice ministry's permission before investigating possible violations of Article 301.
The amendement would also refer to the crime of denigrating the "Turkish nation" instead of the currently used term "Turkishness" which is viewed as too vague.
Hrant Dink, an ethnic Armenian journalist who was gunned down in 2007, was prosecuted under Article 301 for referring to the mass killings of Armenians by Turks in the early 20th century as genocide.
Dink's alleged killer was a teenager influenced by extreme nationalists, and mourners attributed his death to the atmosphere of animosity surrounding the journalist's legal problems.
Dink had received numerous death threats.
Pamuk, who won the Nobel literature prize in 2006, also went on trial for comments on the mass killings of Armenians, but the charges were later dropped.