Two men forced their way into his home in Halsall, near Southport, on Wednesday night (local time) and demanded cash and jewellery.
Moores, 69, was assaulted during the raid and later taken to Aintree Hospital with leg and head injuries. He is said to be in a stable condition.
The offenders made off with jewellery and watches.
Lancashire Police are appealing for information about the burglary which took place at about 8.45pm local time.
Detective Inspector Marc Nasser said: "We believe this was an isolated, targeted attack and I would like to reassure local residents that we have stepped up patrols in the area.
"The investigation remains in its early stages but if you have any information that could assist us, please do get in touch."
Moores, who was chairman from 1991, sold his stake in the Premier League club to American investors Tom Hicks and George Gillett in 2007, a decision he said he later regretted. He is the honorary life president of Liverpool FC.