In a victory speech briefly interrupted by protesters calling for a ceasefire in Gaza, Mr Suozzi said, "This race was fought amidst a closely divided electorate."
He focused on unity and healing political differences, saying: "it's time to find common ground and start delivering for the of America".
CBS, the BBC's US partner, reported that with 87% of the estimated vote tallied Mr Suozzi had 54%, while rival Ms Pilip had 45%.
The election marks a return to Congress for the Democrat, who previously served three terms in the US House but opted in 2022 to run for governor in New York instead.
That bid was unsuccessful, and voters replaced him in Congress with Mr Santos.
With a campaign slogan of "Let's Fix This," Mr Suozzi embarked on a well-funded effort to reclaim his district. He pitched himself as an experienced leader - one whose biography voters already knew well.
Ms Pilip, the Republican candidate, conceded the special election race on Tuesday evening in a speech to supporters.
"We are fighters, I called my opponent and congratulated him," she said.
Eric Adams, the Democratic mayor of New York, said Mr Suozzi's victory "was good news"for the city.
While Mr Santos's historic expulsion from Congress was allegations of corruption, fraud and misuse of campaign funds, the race to replace him was high-profile issues likely to matter in the upcoming presidential contest.
Those included immigration, the Israel-Gaza war and abortion.
Both candidates and their backers poured millions of dollars into a campaign to hold the seat for only a few months. Mr Suozzi will have to run for a new term this November.
New York's third congressional district covers a diverse electorate, stretching from the New York City borough of Queens into the western suburbs of Long Island.
Despite registered Democrats outnumbering registered Republican voters there, polls indicated the race was extremely close for most of the short campaign.
Ms Pilip, an Ethiopian-Israeli immigrant and observant Jew who was hand-picked to run by Nassau County's powerful Republican political machine, made immigration and unwavering US support of Israel central to her campaign.
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