Yes, you will want to pay the estimated tax for your ROTH IRA contribution in the quarter you received it to avoid the penalty. When you receive a taxable distribution from an IRA you have the option to have tax withheld from it by the IRA custodian to be remitted directly to the IRS. In fact, by default the custodian will withhold 10% of the distribution. However, you can instruct the custodian to withhold either 0% or more than 10%, up to as much as 100%.
See Estimated Taxes: How to Determine What to Pay
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