The ailing giants then lost 3-0 to the side from Santa Fe - with Alves quitting as a result - to remain in the bottom three with the worst defence in the Argentine Clausura championship conceding 27 goals in 13 games.
Boca, four-times South American champions between 2000 and 2007, thought they had turned a corner when they emphatically beat arch enemies River Plate 2-0 at home in their big derby, the "Superclasico", two weeks ago.
Veteran striker and captain Esteban Fuertes put Colon ahead in the 15th minute and midfielder Lucas Bertoglio added two more. Boca's Colombian defender Breyner Bonilla was sent off in the 89th for a bad lunge at Bertoglio.
Striker Gaston Fernandez appeared to use his hand to help himself to the early goal from Veron's free-kick in the fourth minute.
Independiente lost for the first time in eight matches on Wednesday when Gimnasia-La Plata's Colombian teenager Marco Perez scored twice for a 2-1 upset win.
Tigre striker Carlos Luna scored twice in their 3-1 win over bottom team Atletico Tucuman on Tuesday to join Mauro Boselli of Estudiantes at the top of the scoring chart with nine. Gimnasia's Perez is next with seven.
