The Football Association of Wales (FAW) will vote for Prince Ali bin al-Hussein in the Fifa presidential election.
Jordan's Prince Ali is the only challenger to current Fifa president Sepp Blatter.
The election will take place on Friday as planned despite the arrest of seven Fifa officials on charges they received more than $150m (£100m) in bribes.
Before the vote, a proposal by the Palestinian FA to suspend Israel from international football was dropped.
Such a vote could have had implications for Wales, who are in the same group as Israel in the Euro 2016 qualifiers.
Palestine, which has been a Fifa member since 1998, had wanted the governing body to expel Israel over its restrictions on the movement of Palestinian players.
It had also opposed the participation in the Israeli championships of five clubs located in Jewish settlements in the occupied West Bank.
But Palestine FA president Jibril Rajoub told the congress he had been persuaded to back down.
"I decided to drop the suspension but it does not mean that I give up the resistance," he said.
Wales are currently second in Group B behind leaders Belgium, who they face on 12 June in Cardiff, on goal difference.
If the Palestinian FA had put forward the proposal and it had been passed, then Wales could have had their 3-0 win against the Israeli's in March wiped out.
Meanwhile, Blatter, 79, is seeking a fifth term as president, ignoring a request to quit by Uefa chief Michel Platini.
The FAW confirmed it had declared for Prince Ali after attending a meeting of Uefa nations on Thursday. Uefa, which governs European football, decided on Thursday not to boycott the election and will continue to back Blatter's rival.
Jonathan Ford, FAW chief executive told BBC Wales: "We believe change is needed in Fifa.
"As you have seen in the press over the last few days, I think its prescient to the fact that our support hopefully together with the support of every Uefa nation, as well as other confederations, will ensure changes do happen and we see changes for the good in Fifa."