Yes! You can pay into your pension through business contributions through your limited company. This means that these business/employer contributions will be offset as a business expense and will not be charged corporation tax, which means less tax will be deducted from your total company's earnings (dividends).
If you pay into your pension through your limited company like this, your contributions will not receive the government's 25% tax top-up, because you have not paid tax on them.
Read our How much can a company contribute to a director's pension? guide for more information!