Zapata's first came from the spot after 40 minutes to cancel out Atletico's 14th-minute opener from Oscar Carniello.
Roman Martinez completed the turnaround in the 72nd minute before Zapata grabbed his second seven minutes from the end.
Goals from Rodrigo Mora in the 45th and 70th minutes gave River Plate a 2-0 win over rock bottom Union Santa Fe.
It was not all good news for River, though, as Cristian Ledesma was sent off six minutes from the end.
Denis Stracqualursi bagged a brace to lead San Lorenzo to a 4-0 win over 10-man All Boys.
Stracqualursi opened the scoring from the spot after 22 minutes but the hosts had to wait until the 63rd minute for Walter Kannemann to add the second.
Patricio Toranzo was sent off a minute later and San Lorenzo took advantage with further goals from Stracqualursi (72) and Luis Aguiar (88).