Newcastle had led from the hour mark through Michael Owen's first league goal since the strike against Everton on October 9.
But Kevin Keegan's hopes of a first win since his return to the club, disappeared three minutes from time with Robert Huth's first goal of an injury-ravaged season.
It was probably the fairest result as both sides were left to bemoan disallowed goals.
Owen had the ball in the net after just five minutes, when Mark Schwarzer dropped an Emre corner and Owen poked the ball over the line only for a foul to go against the England striker.
The remainder of the first half was a dire affair as Boro packed the midfield looking to hit Newcastle on the break and never troubling Shay Given.
It was different after the break and a superb Fabio Rochemback ball over the top put Jeremie Aliadiere in the clear, but he was let down by poor control.
Stewart Downing then cut in from the right to force an excellent full-length save from Given and from the rebound Gary O'Neil, from a tight angle, drove straight at the keeper.
Newcastle had Emre back after a three-match suspension and playing his first game for Keegan. It was the little Turkish international who helped unlock the Boro defence, when his inch-perfect free kick from the left saw Owen unexpectedly out-jump Huth and David Wheater to head beyond Schwarzer.
Newcastle, yet to win in the league this year, upped their tempo and both Owen and Damien Duff had efforts disallowed.
But the warning signs were there when Stephen Carr needlessly lost possession, allowing O'Neil to break clear only to fire wide with just Given to beat.
Boro threw caution to the wind and pushed more players forward and it paid dividends three minutes from time, when Julio Arca's right-wing cross found Huth and the German's looping header dropped over the stranded Given.
Boro then thought they had won it in injury time when Downing's free-kick crashed against the upright and Aliadiere lashed in the rebound, only to be ruled offside.
While both managers were disappointed not to have won, Boro were the more content as they stretched their unbeaten run to six games.