A Finnish woman was also kidnapped from the guest house run by Swedish charity Operation Mercy, with no group so far claiming responsibility for the attack late Saturday.
In a further sign of violence roiling the country, 20 Afghan policemen were killed early Sunday when Taliban fighters stormed their outposts in the southern province of Zabul, as the insurgents escalate their annual spring offensive.
The country's interior ministry confirmed the brazen Kabul attack, the latest in a series of assaults on aid workers in Afghanistan.
"A Finnish lady was kidnapped from police district (three) last night at 11.30. A German lady and an Afghan guard were killed," interior ministry spokesman Najib Danish said on Twitter.
The foreign ministry in Stockholm confirmed that a Finnish citizen has been kidnapped, adding that they were investigating the incident in coordination with their counterparts in Kabul.
"At the moment, the identity of the kidnappers in not known. Finland urges immediate release of the kidnapped person," the Finnish ministry said in a statement.
Operation Mercy's director Scott Breslin told local news agency TT that he was holding a crisis meeting over the incident.
"We know that she's missing, we will send out a press release later," Breslin said in a brief statement.
Operation Mercy is known to work with local Afghan communities in areas such as reducing infant mortality and women's empowerment.
The kidnapping of foreigners has been on the rise, but the threat of abductions is even greater among Afghans.
Kabul is plagued by organised criminal gangs who stage abductions for ransom, often targeting foreigners and wealthy locals, and sometimes handing them over to insurgent groups.
Stinging blow
The violence underscores the deteriorating security situation in Afghanistan, which is in the grip of an insurgency waged by the Taliban and other groups.
The Taliban claimed responsibility for the coordinated attack in Zabul's Shah Joy district, which marks another stinging blow to NATO-backed Afghan forces.
Local officials made desperate calls to Afghan television stations to seek attention as they were unable to get hold of senior authorities for help, highlighting the disarray in security ranks.
"This morning, a group of Taliban fighters armed with heavy and light weapons launched coordinated attacks on several police checkpoints, killing 20 policemen," provincial governor Bismillah Afghanmal told AFP.
A district official told AFP that at least 15 others were wounded in the fighting.
The raid, the latest in a series of brazen Taliban assaults, underscores the insurgents' growing strength more than 15 years since they were ousted from power by the US invasion of 2001.
Taliban militants launched their annual "spring offensive" in late April, heralding a surge in fighting as the US tries to craft a new Afghan strategy and NATO considers sending more troops to break the stalemate against the resurgent militants.
Aid workers in particular have increasingly been casualties of a surge in violence in recent years.
Judith D'Souza, a 40-year-old Indian employee of the Aga Khan Foundation, a prominent NGO that has long worked in Afghanistan, was rescued last July nearly a month after she was abducted near her residence in central Kabul.
D'Souza's abduction came after Katherine Jane Wilson, a well-known Australian NGO worker, was kidnapped in April last year in the city of Jalalabad, close to the border with Pakistan. Wilson was released in March this year.
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