The Netherlands midfielder struck a superb equaliser just 90 seconds after Rafael Leao had opened the scoring for Milan at the end of the first half before converting a penalty in the second period.

Atalanta’s surprise win secured it a semi-final tie against Fiorentina and is the second time it has beaten Stefano Pioli’s side in just over a month, after a 3-2 home Serie A victory on 9 December.

The Rossoneri entered the cup tie in top form, winning five and drawing one of their six matches in all competitions since their league defeat to Atalanta, but the visitors fully deserved to progress.

A first half of few chances burst into life just before the interval when Leao combined with Theo Hernandez at pace down the left and brilliantly converted the latter’s ball inside from the edge of the penalty area.

Atalanta’s response was immediate. With the clock ticking into first-half stoppage time, Emil Holm burst clear on the right edge of the area and his pin-point cut-back was expertly swept home by Koopmeiners.

The visitors then went close to snatching the lead when substitute Mario Pasalic’s effort was blocked by Milan captain Davide Calabria.

Up until a frantic finale to the first half, Milan midfielder Yunus Musah was the only player to have a shot on target, with his 19th-minute shot saved by Marco Carnesecchi.

Milan defender Matteo Gabbia and Atalanta midfielder Marten de Roon had both been forced off following a heavy 38th-minute collision and replaced by Simon Kjaer and Pasalic respectively.

Koopmeiners forced Milan goalkeeper Mike Maignan into a fine low save with a low effort from outside the box at the start of the second half and threatened again as he fired wide soon after.

Atalanta were awarded a penalty – confirmed by the video assistant referee – after Aleksey Miranchuk went down under Alex Jimenez’s challenge and Koopmeiners converted into the bottom corner in the 59th minute.

Carnesecchi turned away Christian Pulisic’s goalbound shot from the edge of the area as Milan chased an equaliser.

Musah’s long-range shot was also saved by Carnesecchi and Milan substitute Jan-Carlo Simic headed wide from a late corner as Atalanta held firm.

The visitors were given a scare in stoppage time when VAR checked for a possible handball moments before the final whistle, while Milan’s unused substitute Antonio Mirante was shown a red card as the players left the field.