Two days is a short enough time interval to get acquainted with the city, so I can recommend to you the following route (it is not ideal, but allows you to see quite a lot of sights):

First day

TopKapa Palace (I recommend that you skip the inspection of Harem), St. Sophia, Yerebatan-Saray, the Blue Mosque. Further, either stay in Sultanahmet and inspect the Hippodrome square, or take a taxi to Dolmabahce. In the evening, you can visit one of the entertainment clubs such as OrientHouse or the like, or make a journey through the evening Bosphorus.

Second day

I recommend to inspect the main mosques: Fatih, Sulejmaniye, Kerie.

The route does not involve visiting the Asian part of Istanbul, as you are very limited in time.