She was greeted by cheering children and celebratory gunfire as she crossed the finish line yesterday at the end of her South American adventure.
The 26-year-old broke a number of world records as she became the first woman to achieve the feat.
Skelton set off on January 20 near Nauta in Peru, and finished 2,010 miles downstream at Almerim in Brazil.
Despite never having been in a kayak before starting training, she paddled around 60 miles a day for six days a week to reach the target, enduring blisters, heatstroke and anacondas.
Sport Relief will take place from March 19 to 21 and will raise money for charity schemes in the UK and developing countries.
It will kick off with a night of entertainment on the BBC, including a new sketch from Gavin and Stacey star James Corden and special editions of Masterchef, Top Gear and A Question Of Sport.
Other celebrity challenges include rugby ace Lawrence Dallaglio cycling around the Six Nations and One Show presenter Christine Bleakley taking on a water skiing challenge across the English Channel.
Skelton said: "It's been a massive adventure that's thrown up challenges most days. It's been tough but I've had enough highs to make it more than worthwhile.
"My bottom is bruised, my shoulders are sore and the muscles in my neck are making it hard to differentiate between my head and my shoulders but to be honest I am proud of the war wounds.
"I reckon that you shouldn't shy away from things because they're tough or you might fail. Get stuck in and you never know where you might end up."
She made more than one million paddle strokes, paddled for 366 hours, drink 320 litres of fluid drunk, used 50 metres of medical tape and suffered 150 insect bites. She set two Guinness World Records – for the longest solo journey by kayak and the longest distance in a kayak in 24 hours by a woman.