The winner of two stages at this year’s Vuelta a Espana seized the lead on the final climb during Saturday's third stage after Wout Poels crashed in the last corner.
The Colombian started the final stage - a short circuit race around the Yas Marina that was won by Team Sky's Elia Viviani - with a 16-second advantage over Vuelta winner Fabio Aru (Astana) and 27 seconds over Poels. Chaves finished safely in the bunch to take his first professional stage race overall win.
"First a mountain stage win, then my first general classification in a professional stage race. I am very, very happy," Chaves said in a statement released by his team.
"To win the first Abu Dhabi Tour is beautiful. It is the first edition of the race, and my first GC too," he said. "I'm happy for the team, and the team is very happy for me."
Orica-GreenEdge Sport Director Matt White said the win marked a huge step forward for the 25-year-old rider who finished fifth this year in the Vuelta.
"It's obviously a great time for Esteban. It's no surprise that he is moving very well here but it's a great sign of things to come," White said.
"It's also a nice way for him to cap off what has been a been breakthrough year for him. He has had some great wins in the past with us, but to finish top five in a Grand Tour and win a stage race in the second part of the season is certainly just reward for all of the hard work he has put in over the last few years."
Chaves indicated his win will provide extra motivation as he prepares for 2016.
"As I follow my winter training program, I will be remembering this race," he said.