Kelly led McSally 53% to 46%, with 82% of the expected votes counted, as of early Wednesday morning, The Associated Press reported.
While Kelly assured his supporters that he was confident in the election's preliminary results, the McSally for Senate campaign did not concede, with not all votes counted.
"Like Mark said, every vote should be counted. With one million votes to be counted and no Election Day results reported from Maricopa County, the decision to make a call at this point is irresponsible," Spokeswoman Caroline Anderegg said in a statement. "We will continue to wait for votes to come in. This race is not over.”
Kelly, a former NASA astronaut, had led McSally by a sizeable margin over the last few months in a contentious race. The newcomer will be set to take up the mantle on Nov. 30.
Speaking with Fox News on Tuesday, Kelly said what Arizonans needed was a unity candidate, and that he felt "pretty good" heading into Election Night.
Following his victory, Kelly addressed a crowd in Tucson, saying he was confident in his win and that his campaign is going to be successful in his mission.
Kelly referenced former Arizona Sen. John McCain, who died of brain cancer in the summer of 2018, saying his "legacy of service" will never be matched though it “lives on as an inspiration that all of us should strive for.
"What Arizonans need is to be focused on finding common ground and solving the challenges in front of them," he asserted.
"And, those challenges are large. But if there’s anything I learned from my mother, and serving at NASA, and what I learned from Gabby is there is nothing that we cannot achieve if we set our minds to it and work together," Kelly concluded.
The special election garnered national attention as Democrats orchestrated an effort to flip the Senate. It quickly became one of the most expensive races for the upper chamber in modern history.
Following success in the 2018 midterm elections, Democrats were emboldened in Arizona.
Arizona is a key state for 2020 Democratic presidential nominee Joe Biden. Both parties have been tracking a noticeable demographic shift in the state's population of 7.3 million people.
Of those residents, 4.7 million -- or more than 60% -- live in Maricopa County, home to the state's capital city, Phoenix, and the nation's fourth-largest county.
The Fox News Decision Desk has also projected that Biden will beat President Trump in the state, despite the incumbent Republican's seven campaign visits.
An influx of young voters, Latino voters, and the renewed support of White suburban women have boosted both Kelly and the Democratic Party.
They showed up to the polls, with nearly 2.64 million early ballots cast by Monday -- a figure exceeding the total number of votes cast in the 2016 election.
Earlier in the evening, The Associated Press confirmed Democrat Ann Kirkpatrick won the state's 2nd Congressional District.
The last time Arizonans elected a Democrat for president was in 1948.
Though not in politics, the 56-year-old Kelly has accomplished a lot since his years growing up in West Orange, N.J.
In 1993, he attended the U.S. Naval Test Pilot School. His service has since earned him almost two dozen military-related medals of commendation.
In 1996, NASA selected Kelly to be a Space Shuttle pilot.
He has spent more than 54 days in space.
In 2007, Kelly fought off colon cancer and four years later he announced his retirement both from NASA and the Navy.
Since then, Kelly has authored multiple books and co-founded the near-space exploration company World View Enterprises.
In 2013, the couple founded the organization GIFFORDS as well as a political action committee named Americans for Responsible Solutions. The committee's mission is to support the Second Amendment while providing solutions to gun-related violence.
The couple now live in the southeastern city of Tucson. They have two daughters.