“The body was identified by her parents,” police spokeswoman, Ulla Brehm, confirmed.
Three people have been arrested – a woman and two men.
The police forced entry to a barn one kilometre from the cafe from where Holm disappeared.
According to Sweden's Aftonbladet newspaper, police swarmed the building with tracker dogs. “It looked like the dogs tracked a scent,” said a witness.
Lisa Holm, who was named by police on Tuesday, was last seen at a café in Blomberg near Lidköping at around 6.30pm on Sunday after working a shift there.
Lidköping is a small town in a rural area north east of Gothenburg, and is close to two of Sweden's largest lakes. It is around 50km from the teenager's home town, Skövde.
More than 7,000 people disappear in Sweden every year, according to Missing People, but the search for Lisa Holm is one of the biggest in recent years and captured high media attention.
Around 900 volunteers joined the search for the teenager, searching woodland, fields and buildings in the region.