- Rafael Leão (40', 74')
Milan, who on Tuesday reached the Champions League semifinals for the first time since they won the trophy 16 years ago, returned to winning ways in domestic action after they were held to consecutive draws by mid-table Bologna and Empoli.
Stefano Pioli made seven changes to the team that were held at Bologna last weekend when he had one eye on the Champions League clash, with Leao, Brahim Diaz and Junior Messias playing behind Ante Rebic and defender Theo Hernandez also back.
Hernandez was taken down in the box early in the game and Milan thought they would be awarded a penalty, but the referee changed his decision following a lengthy VAR review.
Lecce could have sprung a surprise moments later through winger Lameck Banda, who broke inside the box but his close-range header hit the post.
Leao eventually gave Milan the lead five minutes before half-time from a corner with a towering header that bounced in front of goalkeeper Wladimiro Falcone and into the net.
Despite dominating possession, Milan had to wait until 15 minutes from time for the Portugal forward to double the lead.
The 23-year-old latched onto the ball in the middle of the pitch and set off on a brilliant solo run before striking a low shot inside the box that went in off the post.
With 12th goal of the season Leao became the second Portuguese player -- after Cristiano Ronaldo -- to net more than 10 times in two consecutive Serie A seasons.
Lecce, who have failed to win in eight games since February, stay 16th with 28 points, two points above the relegation zone.
- Daniele Chiffi