All legitimate e-mails were held back when the "large" attack began on Tuesday evening so the spam could be removed, a Virgin Media spokesman said.
E-mails were gradually being delivered now the fault was cleared, he added.
About 200,000 people use the Virgin.net service but well under half of these were affected by the problem, the company stated.
Error messages were displayed when they tried to log on. Virgin Media stressed that no e-mails had been lost.
"All customers are able to access e-mail again now, though due to a large queue of undelivered e-mail messages, there may be a short delay before some e-mails reach customers' accounts."