Centre-half Jones was pushed up front for a long free-kick by Dave Cotterill and found a gap at the far post to bundle home in the 88th minute.
Pools' first effort on target came after 56 minutes when James Poole curled a shot in from distance, which was tipped over by Rovers goalkeeper Gary Woods, who then kept out Steve Howard's header from the subsequent corner.
After Charlie Wyke had curled a shot around the far post, Pools took the lead. Howard had two Rovers' defenders pulling at him in the penalty area and, from the spot kick, full-back Neil Austin confidently netted.
James Harper thought he had levelled when he volleyed into the side netting from 18 yards and goalkeeper Scott Flinders acrobatically kept out Cotterill's long-range shot.
But Jones's equaliser prevented Pools from winning for only the second time this season and keeps them in the bottom two.