Officially, Paolo Cipriani and Massimo Tulli, director and deputy director of the bank, handed in their resignations on Monday "in the best interest of the institute and the Holy See".
The bank's president, Ernst von Freyberg, put their decision down to a need for "new leadership to increase the pace" of bringing the institution "in line with international standards against money laundering."
Religious and judicial specialists on Tuesday said the Vatican had forcibly shed two long-serving chiefs who survived the unceremonious eviction in May 2012 of the former head, Ettore Gotti Tedeschi, purportedly for poor management but amid reports of money-laundering.
Their expulsion was deemed opportune by the Vatican, according to Fiorenza Sarzanini in the Corriere della Sera daily, because Cipriani and Tulli are of interest in an inquiry launched by Rome prosecutors in 2010 into money-laundering.
The investigation is set to wind up in the next few days and will likely see them charged, she said, for "knowingly permitting illicit activities to be carried out."
The police probe began with the spectacular seizure of 23 million euros ($26 million) from the Institute for Religious Works (IOR) -- as the bank is known -- after suspicious cash transfers set alarm bells ringing.
The money was released once the IOR agreed to cooperate in the investigation, but Rome prosecutors continued to investigate Cipriani, Tulli and Gotti Tedeschi.
"With the right connections, anyone for years now has been able to open an account with the Vatican bank and clean enormous sums of money. At the last conclave (to elect the pope), the cardinal electors called for a turnaround," Vatican expert Paolo Rodari wrote in La Repubblica daily.
Cipriani and Tulli are also reported to have close ties to cleric Nunzio Scarano, who worked for years as a senior Vatican accountant, and was arrested on Friday on suspicion of plotting to smuggle 20 million euros of dirty money into Italy from Switzerland.
"The reaction was immediate. The Curia (the Holy See's administrative apparatus) understood that it was no longer feasible to treat the financial problems like the paedophilia ones, upping the number of people transferred and deflecting accusations," Carlo Marroni from Il Sole 24 Ore daily said.
The arrest and clear-out of two of the bank's bigs were "the first results of cure imposed by Pope Francis," he said.
What has been hailed as a potential revolution by many religious watchers began with the appointment mid-June of cleric Battista Mario Salvatore Ricca to oversee the IOR's management -- effectively placing one of Francis's trusted allies in a key position to report to him.
Last week, the 76-year-old pontiff followed this by installing a special five-member commission tasked with investigating the bank and reporting their findings directly back to him personally.
The commission's first report is expected in October, and may spark wider reforms of the murky institute.
Marco Politi, religious expert for Il Fatto Quotidiano daily, said that despite rumours the institution could be scrapped, the pope "does not intend to abolish the IOR, because the Vatican needs a bank, but he wants to return to its initial role."
The IOR, which does not lend money, handles funds for Vatican departments, Catholic charities and congregations as well as priests and nuns living and working around the world.
"The inquiry into Scarano was the straw that broke the camel's back," said La Stampa daily.
Experts are now watching to see if more heads will role at the bank, which has a troubled history, including the collapse of the Banco Ambrosiano, in which the Holy See was the main shareholder, and which had been accused of laundering money for the Sicilian mafia.
The chairman of Banco Ambrosiano, Roberto Calvi -- dubbed "God's Banker" in the press -- was found hanging from Blackfriars Bridge in London in 1982 in a suspected murder by mobsters.
A string of recent reports in Italian media about anonymous accounts at the bank being used by organised crime figures and fraudsters suggest there may still be more fall out to come.