"Of course we are always respecting the rulings of the courts and that is our obligation. That's what we swore to do," Santos said in an interview with Caracol Radio.
Administrative court judge Jose Armenta yesterday said Santos was directed not to enforce the ouster ordered by Colombia's inspector general.
He gave the lawyers of Bogota Mayor Gustavo Petro 10 days to show that their client's rights had been violated.
The inspector general has accused the 53-year-old former leftist guerrilla of violating constitutional principles by ending the awarding of trash collection concessions to private companies.
The action set off street protests by Petro's supporters, but on Monday the inspector general's office reaffirmed its decision, turning down an appeal.
"This is a case where the president of the republic has to stick to the constitution, to the laws, to the institutions," Santos said.