About 550 delegates had been expected to vote in the preselection contest at Caulfield Racecourse on Sunday.
Sources at the preselection say the final result was 234 votes to Ms Henderson, 197 to Mr Mirabella.
Mr Mirabella is married to former federal Liberal MP Sophie Mirabella and is a well-established party figure who previously sat on the Victorian branch’s decision-making body, the administrative committee.
Ms Henderson, who is based in Barwon Heads, was the federal member for Corangamite before narrowly losing her seat at the election this year.
Former Victorian upper house MP Inga Peulich and ex-Dunkley MP Chris Crewther also entered the preselection contest.
Ms Henderson was the early favourite, after she was endorsed by Prime Minister Scott Morrison and Treasurer Josh Frydenberg.
Former Victorian Liberal party state president and powerbroker Michael Kroger also backed Ms Henderson.
After winning the vote, the senator-elect thanked Mr Morrison and Mr Frydenberg for their support but also praised the hundreds of delegates who turned out for this “very important democratic process”.
Her appointment to the federal senate must now be ratified by the Victorian Parliament.
“My intention is to hit the ground running, to work incredibly hard for the Liberal Party, for the members who have selected me today and for the people of Victoria,” she said.
In the lead up to the vote Ms Henderson’s internal opponents sought to damage her conservative credentials by dredging up opinion pieces she wrote more than 10 years ago criticising former prime minister John Howard.
It came as Mr Mirabella’s critics moved to undermine his campaign by questioning his residential status and whether he spent more time at his farm near Wangaratta or inner Melbourne.
Former premier Denis Napthine confirmed he had supported Ms Henderson in her bid for the Senate spot, describing her as a “proven campaigner”.
Mr Napthine said Ms Henderson had committed to setting up offices in rural and regional Victoria.
“We need to make sure we have a better spread of our senators across Victoria and Sarah will be doing that,” he said.
In a tweet, Mr Frydenberg congratulated Ms Henderson.
“It will be great to have her back on the team, promoting Liberal values and delivering for all Victorians,” he said.
Phones were running hot over the past 48 hours with Ms Henderson’s supporters frantically working to secure the votes of delegates.
Benjamin is a state political reporter
Rob Harris is the National Affairs Editor for The Sydney Morning Herald and The Age, based at Parliament House in Canberra