The Leeds-based rugby union club say Lowes has left “by mutual agreement with immediate effect”.
The former Hunslet, Leeds, Bradford Bulls and Great Britain rugby league hooker was in his second spell as Carnegie coach, having re-joined the club two years ago as assistant to Bryan Redpath before becoming team boss again last summer.
Lowes was in charge of Carnegie in 2013-14, but switched codes back to league – where he had previous spells as assistant boss at Salford and coach of Warrington Wolves – to take over the hot seat at Bradford.
Carnegie finished sixth last season in the Greene King IPA Championship.
A club statement said: “Newly-appointed director of rugby Chris Stirling will lead the rugby side of the business moving ahead with forwards coach Steve Boden promoted to head coach for the new season.”
In the statement, Lowes – who also helps out with Super League side Leeds Rhinos on an informal basis – said: “I would like to thank the staff, players and supporters at Yorkshire Carnegie for their efforts during my time in charge.
“I have had two very enjoyable years since coming back to the club and will always keep an interest in the team.
“I was proud of the players last season for what they achieved in tough circumstances at times and I wish them all the very best for next season.”
Stirling added: “On behalf of everyone connected with Yorkshire Carnegie, I would like to thank Jimmy for his commitment and dedication to the club throughout both his spells here.
“Our preparations for a big campaign in the Greene King IPA Championship season are well underway now and we are looking forward to that challenge.”