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The 35-year-old said that he wished he could play until his contract with Brazilian club Fluminense expired at the end of the year but realized it wouldn't be possible to continue because of the injuries.
"I wished I could help Fluminense a lot more, but my body didn't let me do it," he said in a statement.
The talented midfielder played in two World Cups and two European Championships with Portugal.
He won the Champions League with FC Porto in 2004 and with Barcelona in 2006.
The retirement comes before a hearing at Brazil's sports tribunal for failing a doping test earlier this year.
Deco tested positive for a diuretic which can help hide performance-enhancing substances.
The playmaker has vehemently denied any wrongdoing and said the result likely stemmed from contaminated vitamins.
He faced a suspension of up to two years in the trial originally scheduled for September.
Deco had four muscle injuries this year alone and played only a few times throughout the season.
He picked up his latest ailment in a Brazilian Cup match at the Maracana Stadium last week. He was returning to action after missing several games but was injured just moments after entering the field late in the second half.
"It's with a lot of sadness that I announce the end of my career as a professional athlete," he said.
"The last minutes I played Wednesday with Fluminense were the last of my 17 years on the field as a football player. I tried my hardest to try to continue playing until the end of the year. My muscles can't take it anymore. I can't keep going."
Deco played only 14 matches this year because of the injuries — three to his right thigh and one to his left.
Deco, who will turn 36 on Tuesday, helped Fluminense win the Brazilian league in 2010 and 2012. He also won the Rio de Janeiro championship last year.
The left-footed midfielder played a total of 686 matches with eight clubs and the Portuguese national team. He scored 116 goals and won 23 titles, including 11 with FC Porto, where he played from 1999-2004. He left Portugal to play with Barcelona, where he twice won the Spanish league.
Chelsea was his last club in Europe.
He left the team in 2010 after winning the Premier League that year.
Deco, whose full name is Anderson Luis de Souza, left Brazil early in his career after not being able to secure a place on some of the country's top teams.
He decided to seek Portuguese citizenship after realizing he was not going to earn a place in Brazil's national team.
He quickly became a regular with Portugal and helped it reach the final of the 2004 Euros and the quarter-final four years later.
Deco began his career with Corinthians in August 1996.
He did not disclose any future plans.
