The 34-year-old has stepped in at the last minute following Flack's announcement on Wednesday that she will stand down as the series host after being charged with assault.
Former MTV host Whitmore will join her boyfriend Iain Stirling, who is the narrator for Love Island, in South Africa where the new series is being filmed.
She said: "To say I'm excited to be heading to Cape Town to host Love Island, the biggest show on television, is an understatement.
"I want to thank ITV for trusting me at the helm of this huge show. I wish it was in better circumstances - Caroline is a brilliant host and also a friend. We've spoken a lot in the last few days since she stepped down.
"She has been very kind to me and strongly pushed me for this role. I've watched her host every series and know I have big boots to fill. I will try and do it justice.
"Above all, I am a massive fan of this show. I've never been to a Love Island villa, and I can't wait to get in there to meet all the new islanders looking for love.
"The Love Island team are the best in the business... including the voice and heart of the show, Iain. He thought he was getting a holiday away from me... not a chance."
Whitmore will host the main ITV2 series as well as its spin-off Love Island: Aftersun, which airs after the main episode.
She also took over from Flack as a presenter on I'm A Celebrity... Get Me Out Of Here! NOW! in 2011.
Flack, 40, was charged last week "following a private domestic incident", reportedly involving boyfriend Lewis Burton.
She announced her decision to step down from Love Island on Instagram, saying "in order to not detract attention from the upcoming series, I feel the best thing I can do is to stand down for series six".
She was arrested in Islington, north London, after an incident about 5:25am last Thursday after reports of a man being assaulted.
Paul Mortimer, ITV's head of digital channels and acquisitions, said he is "delighted" Whitmore is stepping in as host.
He added: "She is the best person for the job and is a popular and experienced presenter of live television. Whilst Caroline is away, we know that Love Island will be in very safe hands."
The new series starts on 12 January on ITV2.