The Bible lists three instances in which the Holy Spirit spoke to the apostles.

As they ministered to the Lord and fasted, the Holy Spirit said, Now separate to Me Barnabas and Saul for the work which I have called them (Act 13:2).

How did He do it? How did He call Saul and Barnabas to special missionary service? The answer is we are not told, and we simply do not know. It was most likely through the means of a special revelation to one of the three teachers who remained. It is also possible that Saul himself received the revelation. The special revelation could have consisted of a vision, a verbal command, or the still small voice of the Holy Spirit.

Similar Account

We have similar accounts where the Holy Spirit is said to have spoken:

Now when they had gone through Phrygia and the region of Galatia, they were forbidden by the Holy Spirit to preach the word in Asia. After they had come to Mysia, they tried to go to Bithynia, but the Spirit did not permit them (Act 16:6-7). And see, now I go bound in the spirit to Jerusalem, not knowing the things that will happen to me there, except that the Holy Spirit testifies in every city, saying that chains and tribulations await me (Act 20:22-23).

Once again, we are not told how the Spirit spoke, only that He did speak.

Don't Exactly Know

Thus, we know that the Holy Spirit spoke to the apostles, but we are not told how He spoke to them.