The fee was not disclosed by either club, though it is widely reported at around €60m (£51.4m) plus performance-related add-ons — a significant outlay for a player Lille signed from Gent for closer to €10m only two years ago.
Fernandez-Pardo made clear to Lille that he wanted the move, and the French club responded by excluding him from first-team training and matchday squads in the closing stages of the window while a deal was finalised. He has signed a long-term contract and will wear the number 20 shirt.
The Belgium international arrives with strong credentials, having started 27 of Lille's 34 Ligue 1 matches last season and scored eight goals as the club secured Champions League qualification. He also featured for Belgium at this summer's World Cup, taking his senior cap tally to five.
Comfortable operating through the middle or from wide areas, he becomes Newcastle's eighth first-team arrival of what the club is calling a transformative summer, and manager Matthias Jaissle's third signing since his own appointment in early August, following the arrivals of Amar Dedic and Nico González.
"I'm really, really happy to be here and very proud to be at such a big club," Fernandez-Pardo said. "I spoke to the head coach and he really showed how much he wanted me to be here.
"In terms of my own career progression, it made complete sense to come so I didn't hesitate at all. I know the club, I know about the stadium, I know it's a fantastic atmosphere.
"I've followed the team. What I've seen is a team that's very ambitious, wants to attack, get forward, really chase teams and go after them, and that's really something I want to take part in as well."
Jaissle was similarly enthusiastic about the signing.
"Matias is a highly technical player with explosiveness in his game," he said. "He can score and assist, he has courage, and he has the ability to take players on. He has already shown in Lille that he can perform on the big stage, and we will work closely with him to keep developing his game further."
Sporting director Ross Wilson described the pursuit as one that had tested the club's patience.
"Matias is a strong example of how a transfer window can unfold with twists and turns along the way. Back in May, he was our top target and we always remained engaged with him," Wilson said.
"A lot of hours went into this one, but we're clear on our Newcastle United identity, and Matias, at 21 years old, has speed, intensity and work rate in abundance. We believe in his profile a great deal."
His arrival also fits into the broader picture of Newcastle's summer business, coming shortly after the club sanctioned striker Nick Woltemade's own departure on loan to Juventus.