The Brazilian club have been awarded the title following last week's horrific plane crash, while Atletico Nacional were honoured with a Fair Play award.
Chapecoense have been named as the winners of the Copa Sudamericana by South American football's governing body CONMEBOL.
Interim club president Ivan Tozzo confirmed at the weekend that the decision had been made following a formal request from Atletico Nacional, who had been due to face Chapecoense in the final of the competition.
The plane carrying the Chapecoense squad and a number of journalists for the first leg of the final crashed en route to Medellin two days before the match was due to take place, killing 71 people on board.
Atletico have been rewarded for their gesture with a fair play prize.
"CONMEBOL's Council has decided to declare Chapecoense as the champions of the 2016 edition of the Copa Sudamericana, as well as grant Atletico Nacional the extraordinary recognition of the 'CONMEBOL Centenary Fair Play' prize," a statement released by the organisation read.
Chapecoense are to receive "all the sporting and economic prerogatives that this entails", CONMEBOL confirmed.
The decision to award Atletico a prize, which includes a cash sum of $1million, came as a result of their willingness to "promote South American football in a spirit of peace, understanding and fair play in the pursuit of sporting values always having prevalence over commercial interests", it added.
Football matches across the world have been preceded by moments of silence in recognition of those who lost their lives in the tragedy.
A tribute was held at the club's Arena Conda over the weekend, attended by CONMEBOL chief Alejandro Dominguez, Brazil coach Tite, the country's president Michel Temer and head of FIFA Gianni Infantino, along with hundreds of supporters.
Last week, Brasileirao clubs issued a joint statement in which they requested that Chapecoense be made exempt from relegation for the next three seasons, while they offered to loan players to the club for free.
Former Barcelona and Chelsea striker Eidur Gudjohnsen has offered to play for the club if needed, while Brazil great Ronaldinho and ex-Argentina midfielder Juan Roman Riquelme have also been linked.
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