First, make an estimated tax payment to cover the taxes before January 15, at www.irs.gov/payments.
Then, when you prepare your tax return, run the penalty section and fill out the penalty form using the annualized method. This will include a form 2210AI with your tax return. This shows the IRS that even though your tax payments were uneven (due to a late lump sum), your income was also uneven and your payments and withholding matched your income in each quarter.