Amazon's home page was inaccessible at 3:35 p.m. PST. It did not become available again until about 4:05 p.m.
Instead of the Seattle-based company's store tabs and welcome messages, Amazon customers received a note saying that the site had experienced a "system error."
"We're sorry. We have encountered a technical problem, which we will investigate," Amazon said in the note to customers. "If you were in the process of placing an order, please note that your order has not been completed."
"We ran two programs at the same time that will not run together," Amazon spokeswoman Kristin Schaefer said. "The combination of the two brought the site down, and we identified the problem and analyzed it."
Amazon suffered a similar 30-minute outage last month, on the day after Thanksgiving. Since then, the site has experienced at least two other, shorter outages.
Schaefer said it was coincidence that the difficulties had hit within such a short time frame.
"Certainly we never want something like this to happen, but unfortunately it does. The systems are up 365 days a year, 24 hours a day, so unfortunately it's going to happen sometimes," Schaefer said.
Reuters contributed to this report.