The row erupted after Bolivia's right-wing interim government accused Spain of attempting to spirit a wanted former aide to ex-president Evo Morales out of the Mexican embassy in La Paz.
Former minister Juan Ramon Quintana has been holed up at the Mexican embassy with around 10 other members of the former leftist government since seeking asylum after Morales quit power on November 10.
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Quintana, another ex-minister Wilma Alanoca and the others have all been charged with sedition and terrorism offences by the new government, which has refused them safe passage out of the country.
But Bolivia was incensed by what it called an attempt by Spanish embassy staff to infiltrate the Mexican mission in La Paz last Friday to extract Quintana, who has been Morales' right-hand man since his early days in power.
"The constitutional government that I preside over has decided to declare persona non grata the ambassador of Mexico in Bolivia, Maria Teresa Mercado, the charge d'affaires of Spain, Cristina Borreguero, and the (Spanish) consul, Alvaro Fernandez," Anez said.
She accused the diplomats of having "seriously harmed the sovereignty and dignity of the people and the constitutional government of Bolivia" and gave them 72 hours to depart.
Bolivia's Foreign Minister Karen Longaric later Monday said the expulsions "do not imply any break in diplomatic relations."
Mexico's foreign ministry denounced the "political" decision and said it had instructed Mercado to return home.
Relations with Bolivia have cooled since Mexico offered Morales political asylum and President Andres Manuel Lopez Obrador called the ex-leader the victim of a coup.
Morales -- who resigned in November after weeks of protests over his controversial re-election -- stands accused of sedition and terrorism and is now living in exile in Argentina.
The Mexican embassy has become the centre of a diplomatic row after it sheltered the ten or so officials from Morales's former government.
Spain hit back within hours, declaring three Bolivian diplomats "personae non gratae" and giving them three days to leave the country.
Earlier, Madrid had issued a strongly worded denial over the alleged attempt to extract the former Morales aide.
"The ministry wishes to clarify that the charge d'affaires was purely making a courtesy visit and vehemently denies there was any aim to facilitate the exit of people holed up inside the building," Spain's foreign ministry previously said.
Mexico's foreign ministry has said the incident occurred as Borreguero and Fernandez wrapped up a meeting with the Mexican ambassador.
But their official vehicles never turned up, and neither of them was able to reach their drivers or their security detail, a ministry statement said.
"On hearing shouting, Ambassador Mercado invited the two visitors to re-enter the residence. At that point, the Spanish diplomats were informed that their vehicles had been stopped from entering."
The Spaniards were advised to leave the embassy on foot but refused to do so without a security detail. Eventually, a Bolivian ministry car was sent to pick them up.
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The presence of former top Bolivian officials inside the embassy has provoked a number of tense exchanges between La Paz and Mexico City.
Bolivia has warned that Mexico will face a "very serious problem" if its embassy refuses to hand over wanted officials, while Mexico has accused La Paz of "harassment and intimidation" for deploying multiple police and intelligence officers outside the premises as well as overflying it with drones.
On Monday, a large police presence continued to monitor activity at the embassy, stopping and checking cars moving through the area, and around 20 activists held a peaceful protest against the Mexican government.
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