Moratti and the Indonesian businessman had been in talks for a number of months, with negotiations thought to have been at a standstill as Moratti refused to allow the Indonesian businessman to purchase a 100 percent stake in the club.
However, a deal has finally been agreed which will see Thohir own 70 percent of the club's shares, and Moratti admitted he was relieved to be leaving the club "in good hands."
"The documents have been signed," Moratti told reporters after putting pen to paper on the agreement. "I find it hard to find the right words to describe how I feel. I just pretend that everything is still normal. Things went fast all of a sudden, but Inter are in good hands.
"Things will possibly change over time, but the important thing is that respect is the base of everything."
Moratti, who took over at Inter in 1995, also suggested he could yet stay on as Nerazzurri president, although no decision over the post has yet been made.
"Will I continue as president? We'll see what happens."
Inter won five Serie A titles, four Coppa Italia trophies and one Champions League under Moratti.