Wrexham shaded the first half but they were struck down by more bad luck as second-choice goalkeeper Callum Burton - who came in for the injured Arthur Okonkwo - was forced off through injury in the 23rd minute. Ryan Barnett, Matty James, Max Cleworth, and Elliott Lee went close for the hosts but Barnsley keeper Ben Killip was in inspired form.
Conversely, Fabio Jalo and Adam Phillips tested Howard in the Wrexham goal in a gritty, low-quality encounter. The Red Dragons, who have the best home form in the division, kept pushing and finally got the breakthrough in second-half stoppage time when Rathbone drove in from 20 yards to send the Stok Cae Ras into raptures.
The result sees the Welsh team, who have won nine of 10 home games this term, consolidate their place in second but now they are just two points behind table-toppers Wycombe Wanderers on Tuesday night.