Yes pay directly online at irs.gov, avoid mailing checks/vouchers if possible. Be sure to designate it as 1040-ES for the correct tax year. When you file under Deductions & Credits there is a section to input any ES paid.
But just paying one-off ES in November may not protect you from a penalty at this point, or may not even be needed depending your situation. See Form 2210 Lines 1-9 for the safe harbor calculation, you need to have paid (via withholding at any time during the year, or "timely" ES - usually quarterly) - the smaller of 100% of your 2024 tax (110% if AGI > 150k or 75k if filing MFS), or 90% of your 2025 tax. If you've already met the safe harbor thru withholding for 100/110% of your 2024 tax then you don't need to pay ES regardless the size or timing of your gains, and just owe the balance of the 2025 tax due in April.
If you do owe ES to meet the safe harbor amount, then by default it's due in quarterly installments so a one-off payment will be considered largely late; it may stop the penalty accruing further but won't eliminate it. If the income occurred unevenly thru the year and in particular later in the year, you can try to reduce the penalty when you file using the Annualized Income method on Form 2210. When you first put your return together TT will calculate the default penalty, check line 38 on your 1040, then you can try and reduce it thru Other Tax Situations / Underpayment Penalties. The other option to avoid ES penalty is to increase withholding to cover the safe harbor amount, it doesn't matter the timing, but it's probably too late in the year for this to have much impact via W2.
See this recent thread for more on the same topic
https://ttlc.intuit.com/community/taxes/discussion/re-paying-capital-gains-tax-on-stock-investments/...
