The visitors' first two goals saw the officials brought into the spotlight but, regardless, the Saddlers were second best throughout and got what they deserved.
Harrogate opened the scoring in the 19th minute as Simon Power's low free-kick found the net, and Matt Taylor's lot could not stem the tide.
Simon Weaver's men grabbed a second as Jack Diamond escaped the offside trap, with Luke Armstrong then putting the result beyond any doubt.
Kieran Phillips struck towards the end but it was too little too late on a hugely disappointing afternoon for Walsall.
Their first League Two defeat in seven leaves them 15th in the table.