The two-day visit came with the Kremlin bidding to strengthen relations with the Arab world's most populous country at a time when Cairo's alliance with Washington has frayed.
Putin is a key non-Arab backer of Egyptian President Abdel Fattah al-Sisi, who has faced US criticism for his deadly crackdown on opponents since he ousted Islamist leader Mohamed Morsi in July 2013.
Their meeting in Cairo follows a 2011 uprising that toppled ex-strongman Hosni Mubarak, whom the Russian leader met on his previous trip in 2005.
Experts say Putin's visit was also aimed at showing he is not isolated internationally despite the crisis in Ukraine, where Russia is accused of fomenting and sustaining a rebellion.
Putin and Sisi made a brief statement after officials signed a memorandum of understanding to build a nuclear power plant in Dabaa on the Mediterranean coast -- Egypt's first such facility.
"If we can reach final decisions, then we can create a new sector in the Egyptian economy based on the construction of the plant, the training of technical staff and development of scientific research," Putin said.
Egypt had taken steps in the early 1980s to launch a nuclear plant to produce electricity in Dabaa but it was shut down after the Chernobyl disaster in 1986.
In 2008 Putin had overseen along with then visiting Egyptian president Mubarak the signing of a deal enabling Moscow to bid for the construction of the nuclear power plant in Dabaa.
The two countries also agreed Tuesday to create a Russian industrial zone along the Suez Canal, whose expansion is a key project undertaken by Sisi.
Putin was received with a guard of honour and a 21-gun salute, while posters of him were plastered on Cairo's main roads greeting him in Russian, Arabic and English.
After arriving on Monday, he and Sisi had attended a concert at the Opera House before dining in the landmark Cairo Tower.
Putin also gave a Kalashnikov assault rifle to Sisi as a gift.
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Russia hosted Sisi's predecessor Morsi during his one-year presidency despite having branded his Muslim Brotherhood movement a "terrorist group" in 2003.
But Moscow was also one of the first countries to endorse Sisi's presidency last year.
Sisi visited Russia when he was defence minister soon after ousting Morsi -- amid deteriorating relations with Washington -- and he followed up with an August 2014 trip as president.
At their meeting last summer at Putin's summer residence in Sochi, the two discussed Russia supplying weapons to Egypt, which is fighting an insurgency in the Sinai Peninsula that has killed scores of policemen and soldiers.
On Tuesday the two leaders also agreed "on further military cooperation between our two countries given the current circumstances" in Egypt, said Sisi.
Putin and Sisi did not take any questions from reporters during their statements, after which the Russian leader left Cairo.
Egypt situation 'alarming'
Moscow has sought to secure a larger slice of the Egyptian arms market after Washington suspended some weapons deliveries in the immediate aftermath of Sisi's crackdown on Morsi supporters.
At the time, Russian media said the two sides were close to signing a $3 billion deal for Moscow to supply missiles and warplanes, including MiG-29 fighters and attack helicopters.
However Washington has since resumed its annual $1.5 billion in aid to Egypt, also delivering Apache helicopter gunships to fight Sinai jihadists.
Egypt's ties with the US still remain cooler than before Morsi's ouster, with Washington criticising Sisi's regime for repressing Islamist as well as secular dissent.
Hundreds of Morsi supporters have died in a government crackdown overseen by Sisi since the Islamist's ouster.
Washington regularly criticises the Egyptian judiciary for handing down lengthy prison sentences to Morsi supporters and secular activists, after often speedy trials.
As long as Washington criticises "Egypt's democratic backslide... it keeps open the door for Putin... to gain influence in Egypt at the expense of US interests," said Anna Borshchevskaya of The Washington Institute For Near East Policy.