The body language will have been instantly comprehensible to any and every Iranian who watched it. At his religious confirmation as Iran’s president on Monday, Mahmoud Ahmadi-Nejad made as if to embrace Ayatollah Ali Khamenei. The supreme leader brushed him aside and the president ended up planting a kiss on his shoulder. It was as if this mercurial and messianic president, eight weeks after the regime convulsed Iran by imposing his re-election on a rebellious people, had been brought to heel.

But appearances can deceive, especially in the opaque world of Iran’s convoluted politics. A never very reliable compass is still spinning. It is not just the broad establishment of the Islamic Republic that has split, with reformists and pragmatic conservatives pitted against fundamentalists and the security apparat. The cohesion of the theocracy has cracked to the point where its core constituents are at odds with each other as well.

On the face of it, a triumphalist Islamist regime has crushed the opposition and reaffirmed the order established by the revolution that overthrew the Shah in 1979. In reality, the Islamic Republic has entered new, barely charted territory. Mr Khamenei, at the apex of the system, has, after all, gambled the legitimacy of the regime by betting it on Mr Ahmadi-Nejad. In so doing, the supreme leader has exchanged the mystique of the office at the heart of Iran’s unique power structure for the role of faction chief.

The standard audit of the balance of power in Tehran is based on the premise that the power wielded by Mr Khamenei – successor to the revered imam, Ayatollah Ruhollah Khomeini – is unassailable. He controls the army, the Revolutionary Guards, the intelligence services, the judiciary and foreign policy. Moreover, a vast network of parastatal fiefs is accountable only to him. A private sector dominated by the Bazaar, a conservative trading community happy to exploit the loopholes in a rigged economy, is held to be in his pocket. The leader further controls both the conventional and traditional mass media: broadcasting and the mosque.

Recent experience shows the theocratic institutions of the Islamic Republic have overwhelmed its proto-democratic redoubts. Thus, under the reformist government of Mohammad Khatami, which tried in 1997-2005 to extend civic freedoms and the rule of law, the Guardian Council and the judiciary struck down more than 100 laws passed by the Majlis, the elected parliament. Under Mr Ahmadi-Nejad, appointed theocrats and Revolutionary Guards have had even freer rein.

But if there were no more to it than that, then a regime that says it won 63 per cent of the popular vote would not need to brutalise its people and stage show-trials against its (still, amazingly) loyal opposition.

Even allowing for the confusing mix of breast-beating and whingeing about conspiracies that punctuates official discourse, the regime’s aggression has reached a new pitch. “Let the swearing-in ceremony occur,” one opposition paper quoted the president railing against his opponents, and “then we will take them by the collar and slam their heads into the ceiling”.

The televised “confessions” of Sayyed Mohammad Ali Abtahi, vice-president under Mr Khatami, and Mohammad Atrianfar, a newspaper editor close to former president Ali Akbar Hashemi Rafsanjani, purporting to establish that Iran has just aborted a western-backed “velvet revolution”, are chilling evidence of how far the theocrats are willing to go.

Their conspiracy thesis is nonsense. Former presidents Khatami and Rafsanjani – the arch-fixer and chameleon of Iranian politics – and Mir-Hossein Moussavi, the former prime minister robbed at the polls after an extraordinary surge of support, are the offspring of the revolution. They seek the reform of the Islamic Republic, not to overthrow it. As Mehdi Karroubi, former Majlis speaker and presidential candidate, told the Spanish daily El Pais this week: “Our dispute is about the elections; we are not questioning the system.”

But that distinction is no longer sustainable. Mr Khamenei’s reckless gamble, and the protean movement of pent-up anger and protest it has provoked, have changed everything. The tattered democratic veil of the republic has been torn away and nothing stands between the regime and a young and impatient people, hungry for change, desperate for jobs and despairing of reform.

The extent of post-election brutality and the loss of legitimacy has now reached very far. Beyond the usual suspects and schismatics, the regime is losing the Bazaar – and the top Shia clerics. Influential ayatollahs, always disdainful of Mr Khamenei’s lack of theological credentials and mostly unconvinced by Khomeinist clerical rule, are fed up of seeing their religion dragged through the dirt of factional feuding. While people in Iran and around the world reacted in horror to the tragedy of Neda Agha-Soltan, captured on video as she was shot dead by a Basij militiaman, the beating to death in prison of Mohsen Rouhalamini, son of a leading fundamentalist, has spread revulsion at the lawless turn of events right into the ranks of the theocrats.

It was not only the usual suspects who boycotted Mr Ahmadi-Nejad’s inauguration and, when the president took a week to obey the supreme leader’s order to fire his vice-president, even some of his hardline supporters threatened publicly to pull the plug on him.

Yet there he is, this pantomime villain out of central casting, with his PhD in traffic management and ostentatious austerity, dangerously dividing the nation. How come?