The retired field marshal took the oath of office at the heavily guarded Constitutional Court and then left to attend a reception with foreign dignitaries.
Western countries alarmed by the brutal crackdown on dissent following the overthrow of Islamist president Mohamed Morsi last year mostly sent low level representatives.
Sisi scored a lopsided victory last month in an election boycotted by Morsi’s Muslim Brotherhood and secular dissidents, also targeted by the army-installed government in the wide-ranging crackdown.
Soldiers and police deployed in force in the capital in anticipation of protests by the battered Brotherhood movement and possible militant attacks.
“I swear by almighty God to preserve the republican system, and to respect the constitution and the law and to care for the interests of the people; and to preserve the independence of the nation and its territorial integrity,” Sisi declared in the ceremony broadcast live on television.
Elite policemen stood guard outside as helicopters dropped posters of Sisi on dozens of well-wishers who turned up to see the former army commander.
“I’m here to congratulate Sisi, the man who rescued us from terrorism and the Muslim Brotherhood,” said one flag-waving supporter, Amira Ahmed.
The presidency said he would later host a reception at Cairo’s Ittihadiya presidential palace, with Palestinian president Mahmud Abbas, Arab royals and African leaders in attendance.
Sisi will also sign a transfer of power agreement with Adly Mansour, a chief justice whom Sisi had installed as interim president when he ousted Morsi on July 3.
Riding a wave of popularity since then, Sisi won the May 26-28 election with 96.9 per cent of the vote against his only rival, leftist leader Hamdeen Sabbahi.
The nature of the victory showed he still enjoyed immense support for his overthrow of the divisive Morsi, after millions held protests demanding an end to the Islamist’s single year of turbulent rule.
But the lower than anticipated turnout of about 47 per cent denied Sisi the overwhelming mandate he had called for ahead of the vote.
The now banned Brotherhood had called for a boycott of the election.
Sisi’s main challenges will be to restore stability and revive the economy after three years of turmoil, following a 2011 uprising that ousted strongman Hosni Mubarak.
Since Morsi’s ouster, the crackdown on his supporters has killed more than 1,400 people and left thousands behind bars, while militants have killed hundreds of policemen and soldiers.
In a televised address after his victory was announced on Tuesday, Sisi called on Egyptians to “work to return security to this nation”.
Sisi’s opponents fear that under his rule, Egypt will return to an autocratic regime worse than under Mubarak.
In the run-up to the election, Sisi said that “national security” takes precedence over democratic freedoms.
He will be the fifth Egyptian president to rise from the ranks of the military, and is expected to reassert the army’s grip on politics.
Saudi Arabia’s King Abdullah, who opposed Morsi’s Brotherhood, called for a donor conference to help Egypt after the results were announced.
The oil kingpin was to be represented at the swearing-in ceremony by Crown Prince Salman bin Abdulaziz, alongside the rulers of Kuwait and Bahrain.
Western nations, which congratulated Sisi on his election win while stressing the importance of safeguarding human rights, sent low-level officials or were represented by ambassadors.
The United States has voiced concerns about “the restrictive political environment” during the vote, urging Sisi to show “commitment to the protection of the universal rights of all Egyptians”.
Senior State Department official Thomas Shannon was to represent Washington at the palace ceremony.