Yes, you can use 'a couple of minutes' instead of 'for a couple of minutes'.
The meaning of the two is very close to being the same, but there can be a very small difference in nuance.
'for a couple of minutes' stresses a little more the time period. Sometimes you may want to do this.
In your example for instance, both phrases are possible, but if you were a little frustrated with the question (They should have given you more time before asking this question !), then the 'for' phrase would be more likely used as it stresses 'it's just been 2 minutes' a little more. It doesn't have to be used, but it would show your frustration better to the person who asked the question.