Usually, when we use the term Yavana, we refer to the Greeks since this is what has been told to us. The Monier Williams Dictionary too gives the meaning of Yavana as Greek.
But then the following blogs tell a different story altogether. This blog says that Yavanas were not Greeks. This blog (you have to scroll down quite a bit) goes further and says that Yavanas were actually Egyptians.
The main Yavana who appears in the Puranas is Kalayavana, the warrior who caused Krsna to construct a whole new city named Dvaraka. He is supposed to be a son of a Yavana Queen by Sage Gaargya, when the King was unable to sire a son.
Personally, I think Yavana maps more to the Greeks, due to Ionia being near Persia, which logically would have been the westward course which Gaargya took had he travelled in that direction. But then the above cited blogs have made me rethink, because one can easily travel southwards towards Egypt as opposed to northwards towards Ionia.
So, were the Yavanas Greeks or Egyptians? Also, did the Greek/Egyptian Pantheon exist at that time? (Since it was only 5000 years ago, I am compelled to say yes, hence the clarification.)