The Abbey Business site was disabled between 9am and 5.15pm, with server issues continuing overnight, preventing users from logging in to the site until midday on 5 July, the company said.
Businesses trying to log on to the site were told there was an error with an Apache-based web server.
"The system problems were caused by a technical error that has now been rectified. The Abbey Business site was not targeted by hackers, and software was not being updated at the time," the bank told Computer Weekly.
"Abbey Business has now resolved the problem.Although we cannot guarantee it will never happen again, we have done everything we can to ensure the site is now fully functional."
Problems with the banking site had a knock-on effect at Abbey call centres across the country, which struggled to keep up with inquiries from concerned customers.
Abbey has 18 million UK and expatriate customers, but was unable to say how many business customers were affected by the problems.
"Where customers feel they have been disadvantaged because of the site's failure we will look at every customer concern individually and deal with each case on its own merit," the bank said.