Macfarlane succeeds outgoing NRC Chairman Gregory Jaczko as head of the agency. Both are Democrats.
The confirmation of Svinicki, a Republican, to a second term and Macfarlane's approval brings to a close what had been a partisan feud over the commission's membership.
Republicans had previously accused the White House of attempting to stall Svinicki's confirmation as payback for criticizing Jaczko's tenure as chairman of the NRC.
A deal emerged in recent weeks with the White House nomination of Svinicki and Jaczko's decision to resign, clearing the way for Macfarlane and Svinicki to move through the Senate in tandem.
The confirmations came shortly after the Senate passed a highway funding bill that also included extensions for federal flood insurance programs and legislation continuing the current interest rate on Stafford loans.
Senate Majority Leader Harry Reid (D-Nev.) had been hoping to pass the highway, student loan, and flood insurance funding package on Thursday, but had to move the vote to Friday after the House did not file a conference report on the highway package Thursday afternoon. Reid waited most of Friday morning for the House to pass the highway package but then decided to go ahead and have the chamber vote on the package even before the House did.
The package passed the Senate in a vote of 74 to 19 and then the House in a vote of 373 to 52. The legislation now goes to President Obama's desk to be signed into law.
Just before it adjourned for a week-long break, the Senate also passed United States-Israel Enhanced Security Cooperation Act of 2012 (S.2165), by voice vote. The legislation is meant to improve "strategic cooperation between the United States and Israel."
Earlier in the day the chamber also passed Sen. James Inhofe's (R-Okla.) Pilot's Bill of Rights (S.1335) by unanimous consent.
Both the Senate and the House approved S. Con. Res. 51, adjourning both chambers until July 9, meaning there would be no pro forma session over the break. The Senate gavels in on Monday July 9 and is scheduled to hold its first roll-call vote on July 10.
The chamber also confirmed almost 30 other military and diplomatic nominations before it adjourned Friday afternoon.