42 MLAs, including leader of Opposition Charanjit Singh Channi, went to the assembly and submitted their resignations.
A resolution to this effect was passed unanimously in a meeting of the CLP in Chandigarh.
The development has come amid a power tussle that polarised the ruling party in the state headed for elections in just about four months.
The shoe flung from the opposition benches fell just short of where Majithia was seated. Protesting Congress MLAs also threw documents including pages from some CAG reports at the speaker, who had to be protected by House staff.
In a blow to Punjab Congress, two of its senior leader resigned from the party and joined the ruling Shiromani Akali Dal on Friday.