Nelson slipped to eighth in the NWC Premier Division as they were leapfrogged by Bootle following a 3-2 reversal on home soil.
With Alex Porter and Paul Fildes injured, Mark Fell drafted in the returning Lydon Hodgkiss and Ben Hoskin.
The Blues had an early chance as Kieran Walmsley loftedthe ball back into the box from a corner, and Peter Wright spun and hit a shot into the side-netting.
Ben Woodhead was called upon to head clear after dashing out of his area at the other end, but the reprieve was short-lived as a Bottle corner was headed out, but returned past Woodhead by Sam Wilkie to give the visitors the lead.
Last-ditch defending prevented Joe O’Neill and Wright equalising, before Wright had an effort ruled out for off-side.
Nelson had an escape when James McGrane hit the underside of the bar, but they went in behind.
They levelled after the break when Matt O’Neill’s shot was parried, and brother Joe pounced on the rebound.
Wright had a shot pushed away by the keeper, before Jake Lloyd was forced off injured, replaced by the returning George Melling.
However, Bootle regained the lead when Mark Kilroy shot through the wall from a free kick and beat Woodhead.
A Bootle snapshot was cleared off the line, but McGrane added a third for the visitors to give them a two-goal cushion.
Hoskin fired what proved a consolation goal for the Blues when his effort hit the underside of the bar and was adjudged to have crossed the line by the linesman.
Tomorrow, Nelson take on St Helens at Ashton Athletic.