The problem struck on Friday evening, causing a delay in activating the Gmail service for end users in newly created Apps accounts.
Google acknowledged the problem on Monday and later said it would have the issue resolved by Tuesday at 3 p.m. Eastern Time.
By Tuesday afternoon, Google had started fixing affected domains, but the work wasn't completed until more than a day later, at around 9 p.m. on Wednesday.
"The problem with the Mail service should be resolved. We apologize for the inconvenience and thank you for your patience and continued support. Please rest assured that system reliability is a top priority
On Tuesday, a Google spokesman said in an interview that after an organization completes the process to transfer its domain to Apps, it typically takes about 48 hours for its end users' Gmail accounts to turn on.
However, for accounts created since around late Friday evening, the activation process took longer due to a Google glitch that slowed down the DNS (Domain Name System) propagation process, he said.
Google Apps administrators reported the trouble in the official discussion forum for the hosted collaboration and communications application suite.
The administrators' impatience stemmed from the fact that once the process to transfer control of their domain to Google Apps begins, they can't access their e-mail until their Gmail accounts are activated.
While the problem lasted, affected users trying to access their inboxes got an error message indicating that the e-mail service was not available. The problem affected Gmail access but not mail delivery, so all messages in affected accounts were routed to their intended inboxes.
Google Apps is a hosted collaboration and communication suite aimed at workplace use that includes various applications, including Gmail. More than 1 million businesses use Google Apps.
Apps' Standard and Education versions are free, while the more sophisticated Premier edition costs US$50 per user per year and includes, among other premium features, a 99.9 percent uptime guarantee for Gmail and access to phone support.
Last week, a Gmail outage that lasted about 30 hours affected some Google Apps customers. Also last week, an unrelated bug affected both the layout and functionality of the suite's Start portal pages in some Apps accounts for about 16 hours.
In August, Gmail had three significant outages and as a result, Google decided to extend a credit to all Apps Premier customers and said it would do better at notifying users of problems.