Zwanziger recently made a complaint to FIFA's ethics committee which led it to investigate the pay and pension arrangements of German football federation president (DFB) Wolfsgang Niersbach, who was cleared of any wrongdoing.
In rare public criticism of one of its own officials, UEFA said Zwanziger had failed to show up at any of its events in the last couple of years and said his conduct was "embarrassing."
"The (UEFA) executive committee is really sad and upset at this situation, it's really not understandable," UEFA general secretary Gianni Infantino told reporters.
"The executive committee fully rejects the actions of Mr Zwanziger," he said, adding his actions were "just to throw a negative image and challenge the financial procedures on the German FA."
Zwanziger was Niersbach's predecessor as DFB president and stepped down from that role in 2012.
An outspoken critic of the decision to award the 2022 World Cup to Qatar, he has been on the executive committee of world football's governing body FIFA since 2011 and his mandate expires in May.
"According to the UEFA statutes, (Zwanziger) represents the European associations, but we have not seen him around in any of our meetings, executive committees, committees, or Congresses for the last two years," added Infantino.
"Part of democracy is to participate in the consultation processes and the discussions and to accept, finally, the decisions which are taken... and not to get angry and upset if it doesn't go the way one would like."
"So we are clearly rejecting his actions, and, anyway, it's all a bit embarrassing for him and sad for German football."
Niersbach told reporters: "I am very disappointed about what has happened. I care about German football and I will use all my contacts, which are not that bad, for the good of German football and as UEFA's representative at FIFA."
(Editing by Ken Ferris)
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