The first leg of the quarter-final tie between the two sides, which ended goalless, was marred by the deteriorating turf on both flanks of the field.
Barca manager Pep Guardiola and several of his players including Lionel Messi, Xavi Hernandez and Javier Mascherano bemoaned the condition of the pitch after the match, and the matter has now been passed on to European football's governing body.
The San Siro, known officially and by Milan's local rivals Internazionale as the Stadio Giuseppe Meazza, is one of the most iconic in world football, but the field has been in poor condition for much of the season.
A brief statement on the European champions' website reads: "FC Barcelona has presented an official complaint to UEFA about the condition of the pitch at the Giuseppe Meazza for the Champions League match against AC Milan.
"They passed the matter over to UEFA delegate Mikalai Varabyov (Bulgaria) at the post-match meeting. Varabyov has included the complaint in his report and UEFA will demand an explanation from the Italian club."