The result assures Milan of progress to the Champions League knockout phase and Ancelotti said: "We had a fine start, took the lead and controlled the game, but the equaliser put things back in the balance.
"We had less energy than Benfica and realised a draw would guarantee our qualification, so we sat back a bit too much in the second half and there were some tense moments at the end.
"Kaka did some wonderful things at the start and end. Alberto Gilardino had more chances in the first half, but then paid the price for the rest of the team not creating as much."
Andrea Pirlo struck for Milan before Max Perreira equalised.
This weekend is a dramatic one for Ancelotti's men, as they welcome Juventus to San Siro in a Serie A showdown.
"We have a game on Saturday that will certainly be tough, as Juventus are in good shape and we have to recharge our batteries very quickly, otherwise we could run into problems.
"Having played six home games and not won any of them in Serie A this season, I'd say this is an excellent opportunity to end that run.
"Our physical condition is good, in general, although we can certainly improve. We have 10 days to prepare for the games in Tokyo and can work then to find our best fitness levels."