Public broadcaster SRF showed footage of the National Council observing the silence during the final day of the summer parliament session.
The president of the parliamentary chamber, Christa Markwalder, also expressed her sadness over the MP's killing in a speech before the final vote on Friday morning.
“In these hours of immense sorrow and disbelief, we wish to extend our sincerest condolences on behalf of the National Council, and… the entire Swiss people,” Markwalder said in English.
“The brutal killing of Jo Cox, our colleague of the British parliament, is an attack on our society's fundamental values and freedoms, principles that we must resolutely defend,” she continued.
“We would like to express solidarity with you and share in your grief. We wish to extend our deepest sympathy.”
Cox, 41, a campaigner for Britain to remain in the EU, was shot and stabbed in her constituency in Yorkshire by a man believed to be a right-wing extremist.
Britain votes on leaving the EU next Thursday.