Check the weather in Israel in September before you book your next holiday. Long-term weather averages give the best indication of the weather in September 2016 and include figures for temperature, sunshine and rainfall for Israel. The September weather guide for Israel shown below is for Jerusalem. Weather in Israel in September. The average maximum daytime temperature in Israel in September is a warm 29°C (84°F) with moderate heat & humidity. There are usually 11 hours of bright sunshine each day, which represents 86% of the 12 hours of daylight.