The discord came to the surface when Egypt on Saturday voted in favour of a Russian-drafted UN Security Council resolution on Syria strongly opposed by Riyadh.
That was followed by Cairo's announcement of Saudi oil giant Aramco's surprise decision to halt the expected delivery of 700,000 tonnes of petroleum products to Egypt this month, forcing Egypt to rush out a call for tenders to make up the shortfall.
Analysts say the row - which threatens to distance Egypt's President Abdel Fattah al-Sisi from one of his main backers - reflects longstanding disagreements on crucial regional issues.
"A strategic alliance means an understanding on regional issues, which is something that does not exist in the Syrian and Yemeni files. The discord now has exploded and risen to the surface."
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Sisi has relied on Saudi support since the then army chief overthrew Islamist president Mohamed Morsi in 2013, with Riyadh since providing billions of dollars in aid and credit.
Saudi King Salman visited Cairo on a rare trip abroad in April, hailing Sisi and approving a slew of investment deals.
Sunni-ruled Saudi Arabia and Shiite-dominated Iran are opposed in a range of regional conflicts and disputes, in particular the wars in Syria and Yemen.
Cairo "does not see the threat of the Iranians" in the same way as Riyadh, said Saudi journalist and analyst Jamal Khashoggi.
"Saudi Arabia tolerated the Egyptian position over and over again, and I think what happened at the UN vote is the straw that broke the camel's back," Khashoggi said.
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