The owner, 41-year-old Mohinder Singh, was killed.
Investigators said there was evidence of quite a struggle and that Singh managed to injure the bandit, who left a trail of blood as he fled from the scene.
A weapon has been recovered, but police have not said what type of weapon.
Relatives told Eyewitness News that Singh worked day and night at the deli to send money to his wife and three children back in India.
Area residents described Singh as a friendly man who was well-known by customers and had a smile for everybody. He owned the deli for several years.
Police said the store does not have a surveillance system. There were apparently no eyewitnesses.
Investigators are urging anyone with information to call 908-654-TIPS.