The air base was shut down in the aftermath of Friday night's coup attempt, but was reopened after talks with the US. Turkey's President Erdogan is demanding the extradition of US-based preacher Fethullah Gulen.
The commander of the Incirlik air base in southern Turkey that is used by the US military and its allies is among the 6,000 members of Turkey's military and judiciary to have been detained by the government.
The government is accusing General Bekir Ercan Van of complicity in last week's coup attempt that, so far, has left more than 260 people dead.
The air base, which is used by US and allied jets to launch strikes against "Islamic State" (IS) militants in Syria and Iraq, was shut down Saturday. Late Sunday the Pentagon announced it had resumed operations at the base.
"After close coordination with our Turkish allies, they have reopened their airspace to military aircraft," Pentagon spokesman Peter Cook said in a statement.
"As a result, counter-ISIL coalition air operations at all air bases in Turkey have resumed," he added, using another acronym for IS.
Erdogan: "Continue cleaning 'virus' from state institutions"
Turkish President Recep Tayyip Erdogan vowed on Sunday to clean out the "virus" within the state bureaucracy. His promise came during a speech at the funeral of victims killed during the coup attempt.
Erdogan accuses US preacher
Erdogan repeatedly criticized his enemy Fethullah Gulen, a US-based preacher who he accuses of being behind the attempted coup.
"They have nowhere to flee," Erdogan said, urging his supporters to continue to occupy public places and take to the streets in the days ahead.
Gulen denies having any connection to the coup.
"As someone who suffered under multiple military coups during the past five decades, it is especially insulting to be accused of having any link to such an attempt," Gulen said in a statement. "I categorically deny such accusations."
Erdogan is demanding the US extradite Gulen, but Washington says it will only do so if given concrete evidence against the preacher.
"We have urged them not to reach out so far that they are creating doubts about their commitment to the democratic process," US Secretary of State John Kerry said during a Sunday morning news program broadcast in America.
Kerry said he had no evidence that Gulen was behind the coup, but urged Turkey to provide any such evidence as soon as possible.
bik/jlw (AP, Reuters, AFP, dpa)