The former PSG and AC Milan midfielder left the Parisian outfit in 2013 after resigning amid a scandal in which he pushed a referee in a Ligue 1 match.
He worked for Milan in the same capacity last season but stepped down due to a disagreement with the side's board.
"This club has been so important to me in my football career and in my life. I had really emotional moments here both as a player in the late 90s and more recently as sporting director," the 1994 World Cup winner said in a statement.
"I come back to Paris full of energy to rejoin this club that I deeply respect," he added.
The Brazilian is back at a club which won the French title last year but failed to reach further than the last 16 of the Champions League and saw the world's most expensive Neymar suspended for hitting a fan after defeat in the French Cup final.
"His return, with his enthusiasm and talent, will bring the club into a new ambitious cycle and I am sure that this reunion will bring happiness to the Parc des Princes, which has always kept 'Leo' in its heart," PSG president Nasser al-Khelaifi said.
Henrique, 51, left his role by mutual consent earlier in the day having seen his relationship with head coach Thomas Tuchel become strained.
He joined PSG in 2017 and oversaw the signings of forwards Neymar and Kylian Mbappe but had been left disappointed by recent transfer windows.