You are on the right track to make sure you can reduce the tax that you will owe next year. The best way to ensure sure you have enough withheld is to use our W-4 Calculator. Gather your most current paycheck stubs to ensure you are making the correct calculations. This calculator also works to estimate your pension withholding, as well. Under the Paycheck(s) section, you will want to select 2 jobs held this year (although one is your pension).
I understand that you have retirement income and also have a job. At the end of the year you end up owing about $2,500.00. The problem is that your employer is withholding taxes based on the employment income. You need compute your total tax liability and then deduct what your employer is withholding. You should make payments of estimated taxes during the year based on the estimated underpayment.
You can submit a W-4 form specifically for pensions, W-4P to your pension plan and update how much they withhold as well. There is a section on the form where you indicate if you have additional income from a job or another pension, etc. Here is the link to the IRS form: https://www.irs.gov/pub/irs-pdf/fw4p.pdf