La Albiceleste had raced to a two-goal lead inside the opening eight minutes but were pegged back by Colombia with substitute Miguel Borja firing in a 94th-minute header.
The result leaves Argentina in second with 12 points from their opening six qualifiers on the road to Qatar 2022, but six points adrift of CONMEBOL leaders Brazil.
"When you think it's all done, no, it's not," Scaloni told reporters post-game. "We're leaving with one point when we deserved all three. Argentina deserved to win.
"Up until the 94th minute, what we were doing was really good and the last play gave them a point, it wasn’t deserved.
"We deserved the three points. I have to congratulate the players because they played a good match in the heat on a difficult pitch against a good opponent."
Argentina did have numerous chances to seal the win including two shots from Lionel Messi which were thwarted by Colombia keeper David Ospina, while Nicolas Gonzalez hit the post in the first half.
Colombia made three half-time substitutions while Luis Muriel was brought on at the half-hour mark to chase down the deficit, with the Atalanta forward netting a 51st-minute penalty.
Argentina's Juan Foyth made an error in the lead-up to Borja's late leveller from Juan Cuadrado's cross although Scaloni refused to criticize him specifically.
"It's individual errors not defensive," he said. "The defensive play of the team was perfect up until that play. It was a specific error and nothing more.
"It's the last play and it changes the entire match. The rest of the 94 minutes and a half were perfect."
Argentina turn their attention to the Copa America which is scheduled to commence on Sunday, with Scaloni's team starting their campaign on Monday against Chile in Rio de Janeiro.