The doctor revealed the man will never be able to have sex again following the operation, although he will be able to urinate after his urethra was moved.
He did not seek medical attention initially but eventually attended hospital when his penis had "turned black".
The man had suffered necrosis, a condition where cells in the body die.
Speaking after the operation, Dr Chirinos said: "We had a 50-year-old patient, that, because he didn't have a girlfriend or a wife, wanted to relieve his sexual frustration.
"So he put his penis in a bottle and this caused the death and necrosis of the penis.
"When he arrived four days later we had to amputate the penis completely because it was completely dead."
He added: "When you put your penis into a bottle it causes a constriction in the blood vessels of the penis and within four hours you can lose the penis.
"This is an embarrassing emergency. The situation with this patient it that he didn't get the medical attention in time and this caused the penis to begin to decay and die completely.
"There was no choice but to completely remove the penis.
"It wasn't just the case here that it had died, it had gone completely black and had begun to decay. The necrosis was very severe."
According to La Prensa, Dr Chirinos also warned men over penis hygiene, stating it should be cleaned three times a day to protect against infections.
