Yes, this is perfectly acceptable.
Company paid pension contributions for the benefit of an employee or director are tax deductible expenses.
To make pension contributions through your limited company you can pay in to a personal pension scheme and receive corporation tax relief on your employer contributions up to £40k for the 2015/16 tax year.
To contribute through your company you need to ensure that payments are made gross as tax relief is gained through corporation tax rather than the pension provider making a claim to HMRC. You should record this as an expense under the category Employee Costs - Pension Scheme Contributions.
The limit for 2012/13 was £50K. You can carry back the employer contributions by 3 years should you not have utilised the allowance.