The company said on Saturday the identity of the second victim must still be confirmed by authorities. One other person was reported dead on Thursday at the time of the accident, which occurred in the Andesita section of the mine.
"This discovery fills us with sadness, but it also tells us that we are in the right place, that the strategy we followed led us to them," Andres Music, general manager of El Teniente, said in a statement.
He said Codelco would continue its efforts with "strength and hope," but with increased caution which could slow its progress.
Music did not provide more details about how Codelco recovered the worker's remains, or update the progress in reaching the area where others are believed to be trapped.
Earlier in the day, Music said Codelco had cleared just over a fifth of the blocked underground tunnels needed to reach the trapped workers, but had not yet made contact with them.
Rescue teams were using heavy machinery, and hoped to proceed at a rate of about 15-to-20 metres every 24 hours, he said, but the exact timing would be unpredictable.
The accident, which took place around 5:30pm on Thursday, was caused by one of the largest tremors ever recorded at El Teniente, with the impact of a 4.2 magnitude quake.
Codelco is investigating whether the cause was mining activity or natural tectonic shifts in the earthquake-prone country.
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