Imam Khomeini summoned a meeting of his colleagues (other Ayatollahs) in Qom to press upon them the necessity of opposing the Shah's plans. Imam Khomeini persuaded the other senior Marjas of Qom to decree a boycott of the referendum that the Shah had planned to obtain the appearance of popular approval for his White Revolution. Imam Khomeini issued on January 22, 1963 a strongly worded declaration denouncing the Shah and his plans.
Two days later Shah took armored column to Qom, and he delivered a speech harshly attacking the ''ulama'' as a class. Imam Khomeini continued his denunciation of the Shah's programs, issuing a manifesto that also bore the signatures of eight other senior scholars.
In it, he listed the various ways in which the Shah allegedly had violated the Constitution, condemned the spread of moral corruption in the country, and accused the Shah of comprehensive submission to America and Israel.
He also decreed that the Nowruz celebrations for the Iranian year 1342 (March 21, 1963) be cancelled as a sign of protest against government policies. In the afternoon of Ashura (June 3, 1963), Imam Khomeini delivered a speech at the Feiziyeh Madreseh seminary in which he drew parallels between Yazid and the Shah and warned the Shah that if he did not change his ways, the day would come when the people would offer up thanks for his departure from the country.
Following Imam Khomeini's public denunciation of Shah Mohammad Reza Pahlavi as a "wretched miserable man" and his arrest, on June 5, 1963 (Khordad 15, on the Iranian calendar), three days of major riots erupted throughout Iran with nearly 400 killed. Imam Khomeini was kept under house arrest for 8 months and was released in 1964.
Also this was a turning point in political viewpoint of Islam.
The clergies had supported Shia monarchy since establishment of Safavids and this was the main source of legitimacy of monarchs. Shia clergies had advised them to be just and obey Ja'fari jurisprudence. Also monarchs didn't enforce religious rules which restricted or threatened religious life and institutions and defended the Shia territory of Iran.
But Reza Shah transformed the Iranian monarchy into a modern dictatorship. The modernizing programs of Pahlavi dynasty restricted and threatened religious life and made clergies be against monarchy and finally Imam Khomeini decide to fight with them and build another state comparable to religious rules.