The court in Istanbul will ask Interpol to issue international arrest warrants for the four commanders, Cihat Gokdemir, a lawyer working on the case, told AFP.
Turkish prosecutors are seeking life sentences for former Israeli military chief of staff Gaby Ashkenazi, former navy chief Eliezer Marom, former military intelligence head Amos Yadlin and former air force intelligence chief Avishai Levy.
The ruling is part of an ongoing criminal trial in absentia of the four men on charges brought by aid group IHH and the victims' families in 2012, which has been denounced as a "show" by Israel.
It also follows months of negotiations between former allies Turkey and Israel to end a diplomatic row sparked following the event.
The ruling could jeopardise reconciliation efforts between Turkey and Israel.
Turkish officials recently said they were close to a deal that would see Israel pay compensation for the deaths.
Local media said Israel had insisted any deal be conditional on the charges against the soldiers being dropped.
Nine Turkish activists died aboard the Turkish-flagged Mavi Marmara, the lead ship in a six-vessel aid flotilla dispatched by Turkish relief agency Humanitarian Relief Foundation (IHH) to break Israel's blockade of the Gaza Strip on May 31, 2010