A fee believed to be £7.1million was agreed between the clubs - as well as personal terms.
However Ba, 25, who needed knee surgery last summer, had now returned to Germany although Pulis refused to divulge what the problem was.
Speaking after the 2-0 victory against Bolton, Pulis said: "I am desperately disappointed. You look at him and he has a tremendous scoring record.
"We have been over to watch him three or four times. Everyone has come back with good reports. But we have to put the club first and I understand that.
"As we have progressed as a club, the medical side has progressed as well. They take great responsibility and great care when they look at the players we are trying to bring in. The money involved is huge. Obviously they found something which could cause problems later."