'was alerted' means that he got an alert. That might have been by one of many different ways - it doesn't say. He may have got a warning from another pilot of another plane. There may have been a weather warning. He may have even seen it on a radar. It may have just been his co-pilot that told him.
This sentence doesn't say what the disturbance was. Was that mentioned somewhere else?
It is similar to 'The captain became aware of the disturbance', but by using 'alerted', the writer is suggesting that someone or something actively informed him, rather than that he just saw it.