Nasdaq said once it became aware of the problem, it halted trading in all Nasdaq-listed securities to "protect the integrity of the markets."
The SIP's technical issues were resolved in the first 30 minutes, Nasdaq added. The remaining time was needed to coordinate with other exchanges, regulators and market participants for an "orderly re-opening" of trading.
Trading resumed at 3:25 pm ET after the longest shutdown at the exchange in recent memory. It halted trading in such high-profile companies such as Apple, Microsoft and Facebook.
Despite the freeze, Nasdaq said that it would not cancel orders.
(Read more: Nasdaq shutdown: Follow the software)
SEC Chair Mary Jo White said in a separate statement the "serious" interruption underlines the need to address "technological vulnerabilities."
The exchange closed at its normal time of 4 pm ET. Despite the troubles, stocks closed slightly up for the day.
(Read more: Nasdaq shuts down, but stock market shrugs it off)
There were reports Thursday morning that NYSE Euronext was telling traders its electronic exchange Arca was having technical issues with some Nasdaq-listed stocks. Nasdaq stopped routing orders to Arca temporarily, but reportedly the issues were resolved before Nasdaq halted all trading.
Nasdaq officials would not comment when asked if the "exchange participant" that had the "connectivity issue" was Arca. The NYSE also had no comment.
Once Nasdaq resumed trading, there were some technical issues when Arca went to reconnect, an NYSE spokesman said. He made the comment in response to a question before the latest Nasdaq statement.