Yes, there are organs that Bach played on which still make music today. Bach Church, Arnstadt, Germany Bach played this organ when he was hired as organist here. Trost Organ of Altenburg Bach inspected this instrument around 1739 and praised it. read more
Unfortunately no there isn't an organ still in use that Bach played. A model organ (der Bach-Orgel) was built in the 21st century that was suitable for his music and contains 61 stops. It is used in Thomaskirche in Liepzig. read more
The Organ at St. Katherine's Church where bach also played was not so fortunate---it sustained some damage when a bomb came through the roof but nevertheless it is still almost as it was in Bach's Time. read more