The pilot, identified by TransAsia as 42-year-old Liao Chien-tsung, has been praised by Taipei's mayor for steering the plane between apartment blocks and commercial buildings before ditching the stalled aircraft in a river.
TransAsia GE235 was carrying 58 passengers and crew when it lurched nose-up between buildings, clipped an overpass and a taxi with one of its wings and then crashed upside down into a shallow river after take off.
The bodies of Liao and his co-pilot were retrieved from the almost-new ATR 72-600's cockpit still clutching the joystick, with their legs badly broken, investigators said.
"They were still trying to save this aircraft until the last minute," Taiwanese media quoted unidentified prosecutors involved in the crash investigation as saying.
Media quoted city officials as saying the death toll would have been much worse if the plane had crashed into any of the buildings it narrowly missed.
Fifteen people survived but 12 remain missing. Taiwan aviation officials have said they have not given up hope of finding them.
The voice and data recorders from the plane have been recovered and a more conclusive picture of the plane's final moments will emerge when information from them is released.
Media reported that some of the information could be released later on Friday.