The 23-year-old will partner Pascal Wehrlein as part of a new-look line-up at Manor Racing - formerly Marussia - for the forthcoming season.
Haryanto has previous F1 experience, having tested for Virgin Racing at the end of 2010, and then for same team, by then renamed Marussia, in 2012 and '15. He also has a prior relationship with Manor, having first driven for them in GP3 in 2010.
"Melbourne will be a huge moment for me, my country, supporters and fans and I want to thank everyone who's been with me since I started in single seaters; 2016 is my chance to reward that faith and represent Asia in F1," Harytanto said.
"Manor Racing is a team with an exciting vision and ambitious plans. They have produced a great package and I can't wait to get in the car."
Stephen Fitzpatrick, Manor Racing's owner, said that Haryanto's performance in GP2 last year - he won three times, took five podiums and finished fourth overall - had impressed his team.
"We are delighted to announce Rio as our second race driver for 2016," Fitzpatrick said.
"Rio's been racing since he first got into a kart at six years old. He's tenacious on and off the track and made a big impression on last year's GP2 battle.
"Rio's huge following in Indonesia is great for the team and for F1. They are keen to see him on the grid and we're confident that we'll see him enjoying some exciting battles in the year ahead."
Manor are expected to make progress in 2016, with a new chassis to compliment a deal to use the class-leading Mercedes power units.
2016 F1 GRID
Mercedes: Lewis Hamilton, Nico Rosberg
Ferrari: Sebastian Vettel, Kimi Raikkonen
Williams: Valtteri Bottas, Felipe Massa
Red Bull: Daniil Kvyat, Daniel Ricciardo
Force India: Sergio Perez, Nico Hulkenberg
Renault: Kevin Magnussen, Jolyon Palmer
Toro Rosso: Max Verstappen, Carlos Sainz
Sauber: Felipe Nasr, Marcus Ericsson
McLaren: Fernando Alonso, Jenson Button
Manor: Pascal Wehrlein, Rio Haryanto
Haas: Romain Grosjean, Esteban Gutierrez