The Istanbul Bar Association filed a criminal complaint against electoral board head Sadi Guven for "wrongful conduct" and "altering the result of the election".
The country's high electoral board announced in a statement they had ruled 10-1 against the move.
Turkish Prime Minister Binali Yildirim, speaking on CNN Turk, urged the opposition Wednesday to drop its challenge.
Turkish police have detained a total of 38 people in İstanbul who took part in demonstrations in protest of a decision by the Turkey's Supreme Board of Election (YSK) to consider unstamped ballots cast in a public referendum on Sunday valid.
On Sunday, Turkey narrowly voted to give President Recep Tayyip Erdogan sweeping new powers and replace their parliamentary system with a presidential one.
"The referendum took place under inappropriate conditions and under pressure from the state of emergency", said HDP Spokesperson Osman Baydemir referring to the ongoing martial law that has been imposed in Turkey's Kurdish southeast.
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"Calling people to the street is wrong and is outside the line of legitimacy", Mr Yildirim said, adding that "we expect the main opposition party's leader to act more responsibly".
"They're the gold standard when it comes to that", she said in reference to the Organization for Security and Co-operation in Europe's Office for Democratic Institutions and Human Rights (ODIHR).
Michael Link, the top election observer for the OSCE, told a group of local German newspapers on Wednesday that Turkish authorities were not cooperating in addressing alleged election manipulation.
Turkish media reported the YSK made the decision to accept unstamped ballots within about an hour after the AK Party filed a petition on election day. "From the German government's point of view, Turkey must ... clear up the questions that have been raised".
Foreign Minister Mevlut Cavusoglu said on Wednesday a critical report by European observers on the referendum contained several mistakes which he believed were deliberate. "After our president and Trump confirmed a meeting in May, [US Secretary of State Rex] Tillerson and I will set a date", Cavusoglu said.
Trump telephoned Erdogan on Monday to "congratulate" him on "his referendum victory" and to discuss last week's USA cruise missile strike on Syria and cooperation in the campaign there against the Islamic State, a White House statement said.
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