James Borg scored the all-important goal for Mgarr.
Meanwhile Ghaxaq joined Mdina in second place after defeating Marsa 3-2 in another match.
In Section B, joint-leaders Zejtun and Naxxar both registered wins.
Zejtun defeated Sirens 3-0 while Naxxar registered a narrow 1-0 win over Kirkop United. Zejtun and Naxxar will be facing each other in a direct clash in two weeks’ time.
On Friday, Attard defeated Swieqi United 4-1 while Gudja United beat Sta. Lucia 2-0.