His sole opponent, Hamdeen Sabahy, received 3.9% of the vote, the country's election commission said. Sabahy conceded defeat last week.
Several thousand people in Cairo's Tahrir Square celebrated Tuesday's announcement. Fireworks erupted overhead as vendors sold Egyptian flags and balloons marked with Sisi's face. Military and security personnel watched from the edges as people danced and sang.
U.S. President Barack Obama plans to speak with el-Sisi in the coming days, the White House said Wednesday.
The United States looks forward to working with el-Sisi "to advance our strategic partnership and the many interests shared by the United States and Egypt," the White House press secretary said in a statement.
The election was called amid months of political turbulence that saw Mohamed Morsy -- the country's first democratically elected president after the ouster of longtime leader Hosni Mubarak -- removed from power in a July military coup.
El-Sisi, who was army chief at the time, stepped down from his military post this year to run for president.
Though Sabahy conceded defeat, he didn't embrace the process.
Allegations were made that his campaign representatives were attacked and detained, and that el-Sisi's representatives were allowed inside polling stations, Egypt's state-run Ahram Online news agency reported last week.
"We cannot give any credibility or ratification to the announced numbers of turnout or results," Sabahy said. "The announced results are an insult to the intelligence of the Egyptians."
The White House said while it is pleased that international observers were allowed to participate in the election, "we also share concerns raised by observation groups about the restrictive political environment in which this election took place."
"As Egypt looks toward parliamentary elections later this year, we urge the government to consider the recommendations of the observer groups on ways to improve the administration of future elections," the White House said.