Is there a word for someone who you've not physically met but know well?

Before the Internet was born, people used to communicate with other people in other places by writing physical letters, mainly for exchanging languages, but also for other purposes, like sharing mutual interests, mating, etc. They'd have their contact details on the related magazines so that the others would've been able to contact them.

That was called a pen friend, or less formally, a pen pal. The alternative spelling for them are penfriend and penpal, without that space in between.

You can check the definitions and articles about these terms on LDOCE and Wikipedia.

Online friend may convey the idea:

• Definition of someone you only chat with on the Internet.

  • An online friendship begins when two people bond and have things in common, just like an offline relationship. The friends may share photos, email each other, or chat on the phone eventually. The friendship can become a source of support and provide emotional benefits even though the friends will never meet in person.

http: www.friendship.about.com

If you're not opposed to a neologism, why not use "e-quaintance" or "ecquaintance"?

In cyber space you can do all kinds of cyber activity, including cyber crime, cyber bullying, cyber security, cyber auctions, cyber attacks, work at your cyber job, obey cyber law, bend to the whim of cyber police, enjoy a journey in cyberquest (jk), find a new job through cyber recruitment, avoid cyber terrorism, attend a cyber university, accumulate cyber wealth, all while making cyber friends.