Nigeria forward Lookman continued his superb form by nodding in his 10th goal of the campaign with three minutes remaining at the Gewiss Stadium in Bergamo.
The 27-year-old met Sead Kolasinac’s flick-on from a corner to give Atalanta a club-record equalling ninth straight win in Italy’s top flight and further boost hopes of a first-ever Scudetto for the traditionally small, provincial club.
Alvaro Morata had looked to have earned seventh-placed Milan a point in a fiery atmosphere with his 22nd-minute leveller after former Rossoneri flop Charles De Ketelaere had crashed Atalanta ahead in the 12th minute with a thumping header.
Napoli host Lazio on Sunday night and Antonio Conte’s team will have to beat the team who knocked them out of the Italian Cup if they are to reclaim their narrow league lead.
Atalanta now turn their attentions to Tuesday’s visit of Real Madrid in the Champions League when they can strengthen their case for direct qualification for the last 16 and get revenge for defeat in the European Super Cup in August.