The world's most expensive player slotted home the 52nd-minute penalty and went over to television cameras by the side of the Stade Pierre Mauroy pitch to make the number 24 with his fingers in honour of Bryant's shirt number.
"It's deeply saddening for the world of sport and for all of us," said Neymar to Canal+ after the win, which put PSG 10 points clear at the top of the league.
"Not just for basketball fans, but for everything he did for sport."
He had already put his side ahead with a fine strike in the first half before putting the game out of reach and increasing the gap between them and second-placed Marseille.
His 12th league goal of the season tipped the balance in the Parisians' favour after a positive start for the home side, who were unbeaten at home ahead of the match.
The Brazilian almost immediately slipped through Mbappe but the onrushing Mike Maignan stopped the France World Cup winner from clinching his 14th top-flight effort of the campaign.
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Mbappe was stopped again by Maignan when he got his body in the way of a fierce close-range effort, but the away side were given a penalty soon after for a clear Gabriel handball just before the forward's shot.
Neymar squeezed his spot-kick just beyond Maignan, who got his hand to the shot but looked on in horror as it made its way in off the post.
"We deserved to win, I think we played well," said PSG coach Thomas Tuchel.
"We controlled the match and counter-attacks and this is not easy to do against a good team like Lille."
Lille stay seventh after the defeat, two points away from the European places.
Neymar's tribute came on what was already an emotional day in French football, with Nantes and Bordeaux also honouring their former striker Emiliano Sala, a year after his death in a plane crash.
The clubs remembered Argentine forward Sala before the Derby de l'Atlantique at the Stade de la Beaujoire.
Bordeaux won 1-0 courtesy of a late goal by Jimmy Briand as Nantes played most the second half with 10 men after the dismissal of Andrei Girotto.
The 28-year-old Sala was killed last January when the small plane taking him to join Cardiff City after being bought from Nantes for £15 million ($19.5 million) crashed off the Channel island of Guernsey.
Nantes wore a special white and pale blue shirt inspired by Argentina while Bordeaux's kit featured an Argentine flag beneath the club crest flanked by the player's initials.
Proceeds from the sales of the strips will go to the two Argentine clubs Sala played for in his youth.
A portrait of Sala was also displayed in the centre circle during the warm-up and there was a minute's applause ahead of kick-off.
Supporters laid flowers outside the ground and broke out into a song commemorating Sala in the ninth minute, representing the shirt number worn by the player which has since been retired by Nantes.
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Sala left his homeland to join Bordeaux in 2012 and then played for Nantes between 2015 and 2019.
Earlier Karl Toko Ekambi scored on his Lyon debut Sunday in a 3-0 victory over bottom club Toulouse.
Cameroon striker Toko Ekambi, who joined on loan this week from Villarreal until the end of the season, sealed the win six minutes later as Lyon climbed up to fifth in Ligue 1.
Toko Ekambi came on as a first-half substitute after a scary incident involving France Under-21 forward Martin Terrier.
Terrier was stretchered off after fainting on the pitch, but Lyon said at half-time the player had regained consciousness.
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