Monaco striker Radamel Falcao was the hero for the home side, keeping his cool to convert two late penalties as Colombia grabbed the point they needed to be certain of qualifying for next year's finals in Brazil.
Brazil qualify automatically for the tournament as hosts, while Argentina had already confirmed their qualification last month.
Falcao's 84th-minute leveller capped an extraordinary turnaroud for Jose Pekerman's team, who had looked dead and buried inside the opening half hour after Chile raced to a 3-0 lead.
However, the sending off of Chile's Carlos Carmona for two bookable offences midway through the second half was to be the catalyst for a remarkable comeback. Teofilo Gutierrez pulled a goal back on 69 minutes to make it 3-1 before Falcao's late show gave Colombia a share of the points.
Chile had earlier looked certain to be heading for a win which would have seen them guarantee their ninth World Cup appearance after a flying start at a ground where Colombia had won their five previous matches.
Juventus star Arturo Vidal fired Chile into the lead on 19 minutes, sending Colombia keeper David Ospina the wrong way with a perfectly placed spot-kick to silence the home crowd.
Barcelona winger Alexis Sanchez then doubled the Chileans' lead three minutes later before adding a close-range second to make it 3-0 on 29 minutes.
Despite the disappointment of failing to wrap up qualification, Chile remain firmly on course for Brazil after results elsewhere worked in their favour.