Manchester City led 2-0 at half time with goals from Raheem Sterling and Gabriel Jesus but sloppy second half almost made them pay.
Brazilian defender Eric Botteghin was ruled out of the Champions League tie between Feyenoord and Napoli.
Milik, capped 36 times by his country, suffered a cruciate ligament injury to his left knee last year which sidelined him for four months. The Poland international injured his right knee late in Napoli’s 3-2 win at SPAL on Saturday.
Scolari, who guided Brazil to their fifth WC in Japan in 2002, took Brazil to the Confederations Cup crown last year.
Napoli are six points behind second-placed AS Roma after continuing their frustrating habit of dropping points against mid-table opponents.
Allegri managed just five wins in 19 league games this season and was fired on Monday morning.
Last years runners-up tops Group F; AC Milan only Italian club in knock-out stage.
Must win match for Napoli while a draw will see Arsenal through
Manchester United,Real Madrid,Paris St Germain,Bayern Munich,Manchester City,Chelsea,Atletico Madrid and Barcelona have safely qualified.
2013 runners-up need to win match against Napoli to stay in contention; Victory enough for Arsenal.
A Cesc Fabregas double helped Barcelona maintain their unbeaten start to the season.
Arsenal are top of Group F but level on points with Napoli,who overcame Olympique Marseille.
There was more misery for AC Milan as it slipped to a 2-0 defeat at home to Fiorentina.
AS Roma extended its record Serie A start to 10 straight wins.
The referee showed a yellow card for simulation each time.