The Italian giants found themselves ahead after 19 minutes when Heerenveen’s left-back Calvin Jong-a-Pin directed a Kaka cross into his own net after it had eluded the keeper.
Gennaro Gattuso scored a rare goal four minutes later to double Milan’s advantage.
The tough-tackling midfielder received Kaka’s low cross with a low shot that went in at the near post from just inside the area.
Filippo Inzaghi made sure of victory on 69 minutes when he controlled Gattuso’s pass inside the area before driving the ball home past the advancing keeper.
The veteran striker became the all-time goalscorer of UEFA club competitions with 64 goals, one ahead of Real Madrid’s Raul.
Danijel Pranjic scored a consolation for Heerenveen with four minutes to go after converting a penalty.
Elsewhere, two-time UEFA Cup winners Sevilla claimed a 2-0 home victory over Germany’s Stuttgart.
Two goals in the space of two first-half minutes from Ndri Romaric and Renato proved enough for the Spanish side.