Multi-millionaire Becker had refused to pay the minister the 9,600 francs (€7,927) he charged for marrying him to Dutch model Sharley Kerssenberg in St. Moritz, Switzerland, complaining it was nearly five times his regular charge of 2,000 francs (€1,651).
"It's a question of principle," he said at a hearing in October last year.
But the Swiss court in Zug where Becker lives said he had to pay - although the judge also ordered the pastor who carried out the June 2009 ceremony to pay towards the ex-sportsman's legal expenses, ATS news agency reported on Thursday.
The minister has been ordered to contribute up to 2,935 francs (€1,977) towards Becker's lawyer fees after the court found he had not provided an itemized bill or fully proven his expenses, ATS reported.
The pastor said he charged more than usual because of the extra work he had to put in for the wedding, including television interviews and trips to Zurich to meet a gospel singer.
The wedding, the three-times Wimbledon champion's second, took place in front of 200 guests at the upmarket ski resort and was screened by German television channel RTL to which the ex-player had sold the rights.