The Ajax coach was furious that the referee opted to award the Rossoneri a last-gasp spot kick for a foul by Mike van der Hoorn.
Stefano Denswil's header in the 90th minute looked to have given the hosts their first win in this season's competition, but referee Jonas Eriksson awarded the Rossoneri a stoppage-time penalty kick after ruling that Mike van der Hoorn brought down Balotelli inside the area.
The Italy international converted the spot kick and preserved Milan's unbeaten record after two games, leaving Ajax third in the group with one point - and De Boer furious.
"It was ridiculous that a penalty was given against us. It cost us two points," the former Netherlands international fumed in his postgame interview. "There are always moments of contact. It is the right time to let go. Van der Hoorn left him at the right moment. Eventually, I can live with a draw, even if the penalty is disappointing."
Van der Hoorn, meanwhile, was was left shocked by his part in the game's late drama.
"The result leaves a very sour taste," he said. "It was great when we scored and thought we would win, but then for me and for the team we still cannot believe they equalized."