Chris Wood's first half penalty - awarded after the impressive Elliot Anderson was upended in the box - separated the two sides at St. James' Park, with Anderson himself going close to adding a second after the break on his first home start for the club.
Eddie Howe's charges dealt well with the threat posed by the Serie A outfit, and they will now take on LaLiga side Athletic Bilbao on Tyneside on Saturday afternoon (3pm kick-off).
United began with intent, pressing at every opportunity, but as is often the case in pre-season, real chances took time to arrive. The visitors' front three of Duvan Zapata, Ederson and Luis Muriel kept Newcastle's backline occupied and the latter flashed one just past the upright before Jacob Murphy replied with a wayward shot of his own.
Nick Pope was starting his first game at St. James' Park since his move from Burnley earlier this summer and was called into action to deny Zapata, who spun and struck a terrific strike which was heading for the roof of the net before the England stopper's smart intervention, tipping it over.
The Magpies looked most likely to create something significant though, and they nearly did when Kieran Trippier combined with Murphy and Sean Longstaff down the right during a sustained spell of pressure just after the half hour. The latter's cross was met by Matt Targett at the far post and his header looked to be dropping either under the crossbar or onto the head of the onrushing Wood, until a timely clearance saved Atalanta.
The resulting corner brought the hosts' opener, however, though it was Anderson who was tripped as he turned in the box. Referee Peter Bankes awarded the spot kick and Wood stepped up to dispatch his first goal of pre-season in confident fashion, firing low into the bottom left-hand corner.
Both Murphy and Anderson pulled efforts wide at the end of the half, and the latter saw another one - a curling strike from the edge of the box after some neat build-up play - turned round the post by Marco Sportiello after the restart. Ryan Fraser was denied from distance too as Howe's men once again started the half with urgency.
Ederson went close with a dipping drive at the other end, reminding the hosts of the threat posed by the Italian side, before the in-form Miguel Almirón - with six goals to his name already this pre-season - went close to making it 2-0, bursting into the box only to be halted by a save from the legs of Sportiello.
Muriel thumped a free kick straight at Pope before Ederson saw a penalty appeal waved away after going down in the box, but Atalanta's threat was somewhat limited following a flurry of substitutions in the second period, with Ederson among those withdrawn.
Howe introduced Matty Longstaff, Matty Bondswell and Dylan Stephenson from what was a largely inexperienced bench but, despite the efforts of Targett who was denied by substitute goalkeeper Juan Russo late on, Wood's goal remained the difference between the teams under the lights at St. James'.
