Scotland midfielder McTominay nodded home his 10th goal in all competitions this season from Giacomo Raspadori's cross in the 72nd minute to save Napoli's blushes after a drab display in northern Italy.
Belgium striker Lukaku has scored 12 times and set up 10 more in Italy's top flight this season and has been key to Napoli's battle with reigning champions Inter for the league title.
The win moved Napoli three points behind leaders Inter Milan, who beat Udinese 2-1, while third-placed Atalanta lost 1-0 at Fiorentina.
Antonio Conte's side are level on 61 points with reigning champions Inter after a largely lacklustre performance which with better finishing would have still been enough for victory on the Venetian Lagoon.
Antonio Conte's Napoli climbed back to within a point of leaders Inter Milan, who came from two goals down to beat bottom side Monza 3-2 on Saturday.
Reigning champions Inter could cut the gap back to three points when they host Fiorentina on Monday.
Belgium striker Lukaku nodded home his eighth Napoli goal from Andre-Frank Zambo Anguissa's perfect cross in the 78th minute to give Antonio Conte's team a statement win in Bergamo.
Georgia striker Khvicha Kvaratskhelia on Friday signed for Paris Saint-Germain for an undisclosed fee from Italian league leaders Napoli, the French champions announced.
Frank Anguissa and Amir Rrahmani scored Napoli's goals in an eight-minute spell in the first half before Andrea Pinamonti cut the deficit early in the second period.
Napoli forward Victor Osimhen struck either side of the break to steer the Italians to a comfortable 3-0 victory over Eintracht Frankfurt on Wednesday and into the Champions League quarterfinals for the first time.
The 11th goal of the Georgian's debut Serie A season came in the 60th minute of Saturday's game, as he slalomed his way into the penalty area and left defenders floundering before burying a fierce finish into the roof of the net.
Napoli striker Victor Osimhen says if he leads the club to first Serie A title in more than 30 years, he will become a club "icon", but he would not be able to reach the status of late Argentine great Diego Maradona.
Matias Vecino's brilliant long-range strike earned Lazio a 1-0 win at Napoli on Friday as the runaway Serie A leaders lost for only the second time in the league this season.
Osimhen tapped in at the far post to give his team a 40th minute lead
Napoli have had an impressive season so far, currently with a 15-point lead over second-placed Inter Milan in Serie A, and have won seven straight domestic league games, scoring at least two goals in each.
Simone Inzaghi's side stay second and are three points ahead of local rivals AC Milan, who beat Monza 1-0 earlier on Saturday, but are a long way behind rampant Napoli after their 2-0 win at Sassuolo on Friday.
It looks only a matter of time before Luciano Spalletti's rampant side secure a Scudetto dreamed of by Napoli fans since the days of Diego Maradona
A 33-year wait for the league crown looks closer to ending for Napoli
AC Milan's crisis threatens to deepen as the champions head into Sunday's derby with Inter, miles off the Serie A title pace and in a battle to reach next year's Champions League.
