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Anyone stuck with Azure AD authentication login for end to end test, here is solution.
you need to have following config in your Cypress.config.js file.
Cypress.config.js
const { defineConfig } = require("cypress");

module.exports = defineConfig({
  chromeWebSecurity: false,

  e2e: {
    experimentalSessionAndOrigin: true,
    experimentalModifyObstructiveThirdPartyCode : true,
  },
});
////////// and this is your test file - login.js (this is example test) . replace 'https://shop.company.com/' with your site url.
describe('Azure AD login solution', () => {
  it('Login with my Azure AD credentials and then redirected back to my main website', () => {
       cy.origin(`https://login.microsoftonline.com/`, () => {
      cy.visit('https://shop.company.com/');
       cy.get('[name="loginfmt"]').type(`${Cypress.env("username")}{enter}`);
       cy.wait(2000);
       cy.get('[name="passwd"]').type(`${Cypress.env("password")}{enter}`);
       cy.wait(2000);
       cy.get('[type="submit"]').type('{enter}');
    });
  })
})