A White House statement indicated President Bush will veto any bill that delays shutting down bases.
Supporters say the $422 billion defense bill is meant to secure the country's military strength and win the Iraqi war.
The Pentagon maintains there's better than a 20 percent excess base capacity that would save billions of dollars if closed.
But opponents say it's bad timing with the war in Iraq continuing.
Among the amendments defeated Thursday was a Democrat move calling for a select committee to investigate prisoner abuse in Iraq.
The Senate debated the defense bill but put off a final vote until after the upcoming Memorial Day recess.