You're right, it does count against your credit limit temporarily, for the days during which they are pending.
If it ever becomes a problem, you can always call your credit card company and:
1) Ask them to temporarily increase your credit limit (though, honestly, just use a different card)
2) Every six months or so, you should be calling your credit cards and asking for credit line increases anyway, provided they don't require a hard credit pull for it.
#2 allows you to avoid this problem and gives you a low credit utilization in general, helping your credit score.
Just my $.02