Rowhani, seen as a moderate in the Islamic republic, made the remarks at a meeting with commanders of the hardline Revolutionary Guards focused on the conflict in Syria, which is Iran's key regional ally.
He said the uprisings in Syria, Libya, Tunisia, Egypt, Yemen and Bahrain, together with the resultant instability, were all "chains of a single plot with one goal," according to state television speech.
The aim was to "benefit Israel, to consolidate Israel and its power" while weakening the anti-Western and -Israeli fronts in the region, where Iran and Syria back Lebanon's Hezbollah and the Palestinian Islamist movement Hamas.
"We know very well that the conflict in Syria is not about which person should be president," Rowhani said.
"It is completely clear that the West has (made) a decision for the entire region as it does not accept our region in its current state."
Tehran says its support for President Bashar al-Assad stems from respect for his status as the elected president and maintains it would back a new leader if he were chosen by the Syrian people.
Tehran has openly provided Damascus with material and intelligence support, but it denies having armed Assad's regime or deployed troops to the conflict.
Iran actively opposes military intervention in Syria, warning of dangerous consequences for the entire region, and stopped short of threatening to intervene if its ally comes under Western attack.
But Guards commander General Mohammad Ali Jafari hinted that his powerful force could intervene.
"If the US takes military action in Syria, it will definitely face numerous problems," Jafari warned. "The Guards will then carry out its duty.