WASHINGTON—Congress passed a short-term extension of government funding and sent the legislation to President Biden’s desk, averting a partial shutdown after resolving a standoff over vaccine rules.

Top Republicans and Democrats reached an agreement on the spending plan Thursday morning to extend funding through Feb. 18, then quickly maneuvered the legislation through both the House and Senate before the expiration of current funding at 12:01 a.m Saturday. The legislation also includes $7 billion for assisting evacuees from Afghanistan.