Jeremy Menez and Giacomo Bonaventura were both on target at San Siro as Napoli's 11-match unbeaten run in the league came to an end.
Milan benefited from lacklustre Napoli defending, with Menez the first to profit in the sixth minute, waltzing his way past three defenders and coolly slotting into the bottom-right corner.
Napoli's defence was caught napping again seven minutes into the second half, Bonaventura rising unmarked in the area and glancing a header beyond Rafael.
Benitez was particularly annoyed with Milan's opening goal and insisted Napoli's problems are not tactical.
"There were four or five players near the ball," the Spaniard told Sky Sport Italia.
"We have two midfielders to close off those corridors and two centre-backs to clean up but it slipped through.
"The issue is not tactical, as if we do what we're supposed to, then we do not concede."
The loss saw Napoli drop to seventh in the standings, level on points with Milan after 15 matches and 12 adrift of league-leading Juventus.
Sampdoria are two points clear in third position and Benitez is aware that Napoli cannot afford to drop more points.
"Clearly we need to win our games to get closer," Benitez added.
"It'll be increasingly tough to get third place but we knew Serie A was a very difficult league."
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