And it was no more than Roger Ashby's side deserved as they more than matched their illustrious opponents.
Borough may be challenging Northwich Victoria and Stafford Rangers for a place in the Conference next season but they are still five divisions below Boro.
It should have been a straightforward tie for Steve McClaren's side but they struggled to impose themselves on their opponents throughout the 90 minutes and now face another game in what is already becoming a hectic schedule.
Boro made the best possible start when Gaizka Mendieta netted with a brilliant free-kick after only 15 minutes.
But Nuneaton refused to be overawed and made a spirited comeback before eventually snatching a late equaliser when Gareth Southgate handled the ball and Murphy slotted home the penalty.
Murphy twice went close in the opening five minutes before Mendieta beat goalkeeper Darren Acton after Terry Angus had given away a free-kick just outside his own box.
Nuneaton lost David Staff through injury after less than 20 minutes before Action did well to deny James Morrison.
Substitute Stuart Whittaker tested Boro keeper Bradley Jones – in for Mark Schwarzer who looks set to leave the Riverside Stadium after having a transfer request granted earlier in the week - with an ambitious effort before Mark Noon curled a shot just wide.
Mendieta and Stuart Parnaby went close to doubling Boro's lead but Nuneaton continued to create chances of their own and Terry Angus, Whittaker and captain Neill Moore all went close.
Nuneaton should have been awarded a penalty midway through the second half when Noon appeared to be held back by Southgate but referee Mike Dean waved play on.
But in the dying minutes Southgate miscued a clearance onto his own arm and Dean sent the home fans wild by pointing to the spot and Murphy duly sent Jones the wrong way with his well-taken penalty.
Nuneaton - Gez Murphy. Kept his cool to grab the last-gasp equaliser but had been a constant threat to his Premiership opponents throughout the game.
Middlesbrough - James Morrison. The youngster added to his growing reputation with another cultured performance in an uninspired Boro display.