Daboll went 20-40-1 in three-and-a-half seasons with the Giants. Giants offensive coordinator Mike Kafka was named interim head coach to replace Daboll.
The Giants squandered a double-digit lead in the final minutes for the second time this season on Sunday in losing at Chicago, dropping their fourth consecutive game.
Daboll was also recently fined $100,000 for violating the NFL's concussion protocol after he entered the medical tent shouting at trainers to get quarterback Jaxson Dart back on the field as he was being evaluated for a concussion.
The Giants also said general manager Joe Schoen will stay in his post and lead the search for a new head coach.
New York went 9-7-1 in Daboll's first season and reached the NFL playoffs, losing to Philadelphia in the second round.
The Giants parted ways with running back Saquon Barkley and quarterback Daniel Jones only to see Barkley spark Philadelphia to last season's Super Bowl crown and Jones lead the NFL in passing yards this year for Indianapolis, which leads the league in scoring.