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If you have documented what he borrowed you can deduct it from his last paycheck. If you do not have it documented, than you are out of luck. You cannot hold his last paycheck or deduct it from his last paycheck.
Well, it will be his word against yours. Are there any witnesses? If it is not signed he can claim you made it up. Do deduct it, you will have to prove it that you gave him the money and he accepted it.