Plymouth-born centre-back Ellis, 28, has made just 12 appearances since joining the Cumbrians from Shrewsbury on a permanent basis last summer.
It is his second spell at the New Lawn, having spent the 2009-10 season with Rovers on loan from Torquay United.
The deal follows fellow defender Charlie Clough's move to Barnet for an undisclosed fee on Monday.
Carlisle United have loaned defender Mark Ellis to Forest Green Rovers for the remainder of the season.