The 49-year-old former Brazil international was sporting director in Paris for two years between 2011 and 2013, before he quit after being suspended by the French Football Federation for pushing a referee.
The Ligue 1 champions took to Twitter to announce the long-expected return of the executive, who had spent the past two seasons in the same position at AC Milan.
"It is always a special moment to see Leonardo return to Paris Saint-Germain," PSG chairman Nasser Al-Khelaïfi said in a statement. “”Leo" has a place in our club’s history and we all know the role he played as sporting director at the start of our project.
"Paris Saint-Germain has always remained his family and we are delighted to welcome him back. 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."
Earlier on Friday PSG and Antero Henrique parted ways by mutual consent, the club announced.
PSG won Ligue 1 in both seasons Henrique was at the helm, but failed to make an impression in the latter stages of the Champions League.
The club thanked Henrique for his service and wished him well for the future.
“Paris Saint-Germain and Antero Henrique have decided to terminate their agreement by mutual consent,” the club statement reads.
“In his two seasons as sporting director since joining Paris Saint-Germain on 2 June 2017, the Portuguese helped the men’s senior team to the Ligue 1 title in 2018 and 2019, the Coupe de France and Coupe de la Ligue wins in 2018 as well as the Trophee des Champions in 2017 and 2018.
“The club thanks Antero Henrique for his professionalism and commitment over the past two years and wishes him all the best for his future projects.”
Henrique’s time in Paris was marked by some startling transfers as PSG looked to become a European super power.
Brazilian forward Neymar joined PSG for a world-record fee of €222m (£200m/$262m) in August 2017.
Henrique and PSG weren’t finished with acquiring top-tier attacking talent there. Then-teenaged sensation Kylian Mbappe also made the move to the French capital from Ligue 1 rivals Monaco.
Initially signed on a season-long loan, the French international made his move permanent on July 1 2018 for a fee of €180m (£166m/$212m).
Henrique was also responsible for the hiring of Thomas Tuchel as head coach at the start of the 2018-19 season, though there has been speculation of a rocky relationship between the two.
It is reported that Henrique has an offer to become sporting director of Chinese club Shanghai SIPG.