Boro had claimed more points per game on home soil than any other side in the division before kick-off.
But, just as they did in their 1-0 victory against Oxford United three days earlier, Wrexham started on the front foot as Sol Brynn denied Ryan Longman in the sixth minute.
After going short from the resulting corner, George Thomason fed Windass, whose shot struck Dael Fry before sailing beyond Brynn.
Wrexham were dealt a blow in the 22nd minute as Lewis Brunt – starting in place of the suspended Callum Doyle – was forced off through injury, with Dan Scarr coming on in his place.
But the Welsh side still carried the greater threat as summer signing Windass had another effort blocked as Boro went into the break having failed to register a shot on target.
Boss Rob Edwards responded by making four substitutions, Luke Ayling, Sam Silvera, Tommy Conway and Alan Browne replacing Matt Targett, Delano Burgzorg, Sverre Nypan and Morgan Whittaker.
His side grew in confidence as Wrexham keeper Okonkwo made a routine save to deny Conway on the hour mark.
Sensing the home side’s improvement, Phil Parkinson sent on Nathan Broadhead, Liberato Cacace and Lewis O’Brien on 65 minutes, with goalscorer Windass, Longman and Thomason making way.
The visitors should have doubled their lead shortly after that trio of substitutions as O’Brien crossed for Kieffer Moore, who headed against the crossbar from close range.
And they were left to rue that miss when Hackney headed home his second goal of the campaign.
Just three minutes later, Okonkwo kept out the midfielder’s free-kick as the hosts pushed for a winner.
But it ended level as Boro extended their unbeaten home record, while Wrexham missed out on back-to-back league wins for the first time this season.
