The NSA, which runs the majority of surveillance programmes, stopped collecting the affected data at 19:59 GMT on Sunday.
The failure to reach any agreement in the rare Sunday sitting of the Senate was the result of the actions of Rand Paul.
A libertarian, Mr Paul used a Senate technical procedure to block an extension of the Patriot Act, arguing that data collection is illegal and unconstitutional.
Two weeks ago, he led a filibuster – using extended debates to delay or block the passing of legislation – to stop the quick passage of the Freedom Act.
On Sunday he said: “This is what we fought the revolution over, are we going to so blithely give up our freedom?”
After the deadline passed, he added: “Tonight begins the process of ending bulk collection. The bill will ultimately pass but we always look for silver linings. I think the bill may be replacing one form of bulk collection with another but the government after this bill passes will no longer collect your phone records.”
His actions have infuriated many other Republicans. They left the chamber en masse when Mr Paul rose to speak.
Rep. Justin Amash chimed in with his support here.