Jaejoong made a low-key enlistment. It is not known where he will receive his weeks-long training before entering active military duty.
He will be discharged from service 21 months later on Dec. 30, 2016.
The 29-year-old singer-actor previously bid farewell to his fans at the two-day concert "The Beginning of The End" at Korea University in Seoul.
Ticket prices for Sunday's show soared to as much as 1 million won ($903) due to avid fans who wanted to capture his last moment before enlistment.
Shortly after his enlistment, Jaejoong will release his second solo studio album, but an exact release date is yet to be confirmed.
Meanwhile Sungmin, who also joined the army Tuesday, is the first idol male singer who is married and was accompanied by his wife - musical actress Kim Sa-eun - on his send-off.
"Kim would see her husband off to the army. He is going to enter the training camp quietly, accompanied with his family," a source close to Sungmin told a local media outlet Monday.
Sungmin and Kim were married in December after they first met during the musical "The Three Musketeers," playing d'Artagnan and Constance, respectively.
Earlier last week, Shindong, another member of Super Junior, also joined the army.
On the day, several fans and media outlets were waiting to see him off, but he quietly entered the training camp without any special fanfare.
In Korea, all able-bodied men aged between 18 and 35 are required to serve about two years in the military to deter threats from North Korea.