Create a "start.sh" in the eclipse root folder, make it executable. then put the following two lines in the files:
export SWT_GTK3=0 ./eclipse
Now launch the "start.sh" instead of "eclipse" executable.
While the above solution seems to temporarily solve the black tooltip problem for me, eclipse will occasionally crash due to issues button size cannot be determined. Today, my colleague comes up with a better solution which is to replace the default desktop environment in centos with the xfce http://www.xfce.org/. This completely remove the issue with black tooltip background in eclipse.