Yes, because the EIN is the same, the IRS treats it as the same employer. You will have to request it from your employer and they can make an adjustment on your paycheck if you still work for them, or you can request directly from the IRS:
Employer's error - If any one employer withheld too much Social Security, Tier 1 RRTA tax, or Tier 2 RRTA tax, you can't claim the excess as a credit against your income tax. Your employer should adjust the excess for you. If the employer doesn't adjust the overcollection, you can use Form 843, Claim for Refund and Request for Abatement to claim a refund.