Excalibur, now dead, howling for his masters, who are quarantined in a Spanish hospital
Activists scuffled with police outside her home as the dog was taken away.
The nurse, Teresa Romero, is the first person known to have contracted the deadly virus outside West Africa.
She had treated two missionaries who later died from Ebola. The virus has killed 3,879 people, mostly in Liberia, Sierra Leone and Guinea.
A court order to euthanise Ms Romero's dog was issued on Tuesday despite uncertainty over whether the animal was also infected or risked spreading the disease.
On Wednesday about 50 animal rights activists held a protest outside the nurse's home in Madrid, shouting "assassins".
Two protesters were hurt when they tried to stop the van in which the animal was being transported, El Pais newspaper reported.
The fate of the dog, named Excalibur, sparked huge interest on social networks, after Ms Romero's husband, who like her is being kept in isolation in a hospital, alerted animal protection groups via social networks.
Ms Romero, 40, was part of a team of about 30 staff at the Carlos III hospital in Madrid looking after Spanish missionaries after they were repatriated from West Africa.
She told the El Pais newspaper that she might have become infected when removing her protective suit after cleaning one of the missionaries' room.
Analysis: Can dogs get Ebola?
Scientists think Ebola first originated in fruit bats, which seem to cope well with the virus and do not become unwell. People can pick up Ebola directly from animals through contact with infected bats or through contaminated bush meat.
In some studies of previous outbreaks dogs were seen to have antibodies against the virus in their blood - proteins that fight Ebola. Their presence suggest the dogs were exposed to Ebola at some point and their bodies mounted a defence against it.
But whether the virus actually causes illness in dogs and whether dogs can then spread it on to humans remains unclear.
Comment: In other words, it doesn't. What the Spanish authorities did was OUTRAGEOUS.
Striking workers
A World Health Organization (WHO) adviser has warned that more Ebola cases can be expected among medical staff, even in developed countries.
In Sierra Leone, burial workers have gone on strike this week, leaving the bodies of Ebola victims on the streets of the capital, Freetown.
Local media said the teams had abandoned their posts in anger over unpaid wages, but Deputy Health Minister Madina Rahman insisted on Wednesday that the strike had been "resolved" and the staff would soon return to work.
In neighbouring Liberia, health workers say they will go on strike if their demands for more money and safety equipment are not met by the end of the week.
In the UK, Foreign Secretary Philip Hammond said Britain could be "proud" of its contribution to the battle against the virus, telling the BBC £125m ($170m) had been committed to the fight already.
He said "rapid construction" of medical facilities was ongoing in Sierra Leone after the UK announced it was sending 750 troops.
Comment: Great, the Brits are joining the Yanks in sending troops to shoot Ebola on sight. Like we should expect anything less from two countries whose answer to everything is WAR.
Meanwhile the first person to be diagnosed with Ebola in the US - a man who contracted the virus in his native Liberia - died in a hospital in Dallas on Wednesday.
The US has announced it will begin screening air passengers arriving from affected countries as soon as this weekend.
This was very cruel, sadistic and without any scientific merit - to take away and murder this family's beloved dog while they're sick or hospitalized. Of course, it's Spain - where they torture, stab and slaughter young bulls for the entertainment of the paying audience as well as stake out their unwanted racing greyhounds on the beaches to drown when the tide comes in or simply hang them from trees in the countryside until they're dead.
If I were this couple, as soon as I was well, I'd be hunting down every scumbag who participated in my dog's murder - those evil psychopaths! As if this plague isn't bad enough on it's own....