The self-employment tax on your wife's self-employment profit is part of the overall tax liability determined on your joint tax return to which your tax withholding is applied.
Increasing tax withholding for the remainder of the year is a far better approach than making late estimated tax payments. Since, by default, tax withholding is treated as having been paid uniformly throughout the year, increasing tax withholding for the remainder of the year will reduce or eliminate the underpayment of taxes earlier in the year whereas making late estimated tax payments will not. Just be sure to adjust your tax withholding again later if need be, particularly at the beginning of next year.
