Both sides were reduced to 10 men midway through the first half when Argentina striker Gonzalo Higuain and Colombia central defender Cristian Zapata were shown the red card for kicking out at each other.
"It got complicated (with the red cards), I don't think they should have been sent off," said Argentina's Angel Di Maria, who had a fine game prompting Argentina attacks.
"We didn't want to draw, we wanted to win but were left with only one striker," he told Fox Sports.
Colombia centre back Mario Yepes said: "(The result) is good for us, we keep adding (points)."
Colombia goalkeeper David Ospina made three crucial saves and the match featured a string of close misses.
Striker Jackson Martinez put the ball in the Argentine net from James Rodriguez's cross in the 20th minute but it was ruled offside, and Sergio Agiuero had the ball in the Colombian net twice in the second half but was denied both times by offside decisions, the second of which was a hairline decision against Messi.
Ospina saved at the feet of Higuain in the eighth minute and Colombia striker Radamel Falcao headed wide from right back Camilo Zuniga's cross in the 12th.
Four minutes later, a poor clearance in the Colombia box had Higuain heading point blank at goal with Ospina parrying the ball and defender Federico Fernandez heading the rebound against the bar in Argentina's best chance.
Messi, having resumed training on Tuesday after three weeks recovering from a hamstring injury, came on in the 57th and immediately wrought havoc in the Colombia box with Ospina sticking out a hand to avoid a defender's own goal.
"I'm not fit. Today I was able to play a bit but I didn't know how my leg would respond," Messi said.
"Ospina was the man of the match," he added.
Claudio Pizarro struck early to hand Peru a 1-0 home win over Ecuador that keeps alive their hopes of reaching the World Cup finals for the first time since 1982.
Pizarro scored in the 12th minute when he controlled midfielder Juan Vargas's cross with his back to goal and sent an overhead kick inside the far post.
The victory saw Peru climb above Uruguay into sixth place with 14 points from 11 matches.
Venezuela are currently in fifth position with 16 points from 12 games.
Chile scored a 2-1 away win over Paraguay at the Defensores del Chaco to give their campaign a boost.
Striker Eduardo Vargas put the Chileans ahead with a shot from outside the box four minutes before halftime before midfielder Arturo Vidal, who had hit the post in the opening minute, doubled their lead in the 56th minute.
Striker Roque Santa Cruz pulled one back in the 88th minute for Paraguay, who are bottom of the group and have virtually no chance of qualifying for Brazil.
Venezuela conceded a late equaliser to draw 1-1 at Bolivia.
Venezuela, who are looking to reach the finals for the first time, went in front when midfielder Juan Arango headed home Richard Blanco's flick-on from a Cesar Gonzalez corner in the 58th minute.
But substitute Jhasmany Campos headed home an 86th minute corner to salvage a 1-1 for the Bolivians at the Hernando Siles stadium, a result that suited neither side.
Bolivia remain one from bottom of the standings with little chance of reaching next year's finals in Brazil.
The top four teams at the end of the qualifiers in October will go through to the Brazil finals. The fifth-placed team will enter a play-off against an Asian qualifier in November for another berth.
- Sports & Recreation
- Gonzalo Higuain
- David Ospina