Australia star Kerr got Chelsea's opener only for Clarissa Larisey to equalise for Hacken in the Group D encounter.
However, Scotland's Erin Cuthbert netted twice in the second half to secure the victory for Chelsea, who leapfrog Hacken into first place with two games still to play.
Paris FC are two points behind Chelsea in third place after their 1-0 victory away to Real Madrid in Spain, secured thanks to a late penalty from veteran Gaetane Thiney.
Real have just one point from four matches and cannot now qualify for the last eight.
Ajax are top of Group C after Romee Leuchter's goal gave them a 1-0 win at home to Bayern Munich.
Paris Saint-Germain are second thanks to their 3-1 victory over Roma in Italy, with Tabitha Chawinga, Marie-Antoinette Katoto and Korbin Albert all scoring.
There is more action on Thursday, including reigning champions Barcelona hosting Rosengard of Sweden in Group A and Lyon visiting Brann of Norway in Group B.
