Nigerian international Yakubu enhanced his reputation as a penalty king by giving Boro a second-half lead but Arsenal skipper Thierry Henry grabbed a late equaliser.
Arsenal defender Philippe Senderos was shown the red card for a professional foul that led to Yakubu scoring his 13th goal of the season. Senderos brought Yakubu down as the last player in defence and was immediately sent off.
Arsenal were full value for a point but the Teessiders can earn credit for a battling performance.
Middlesbrough welcomed Mark Viduka back, but were again without goalkeeper Mark Schwarzer, with a back injury.
Fellow Australian Brad Jones again deputised following his impressive performance at Portsmouth.
Arsenal made six changes from their Carling Cup semi-final tie against Spurs in midweek.
Boro manager Gareth Southgate had urged an attacking policy before the game against the attractive visitors.
In an early Middlesbrough attack Gunners goalkeeper Jens Lehmann raced out of his penalty area to clear with Viduka preparing to break down the left wing.
In another attack Yakubu looked dangerous, but he was checked by Justin Hoyte.
Arsenal were showing slick inter-passing but Middlesbrough were playing with the confidence of a side unbeaten since the turn of the year.
During Arsenal pressure, Middlesbrough centre-half Jonathan Woodgate showed the class that justified a return to the England international scene for the friendly with Spain.
Tomas Rosicky went close for Arsenal with a powerful shot from outside the penalty area, following a headed clearance by Woodgate.
Jones saw the danger after flinging himself full-length to his left as the ball went inches past the far post.
Henry shot from the edge of the penalty area in another Arsenal attack, but Jones dived to his left to save.
It was clear why Middlesbrough had turned down a £300,000 bid for Jones by West Bromwich Albion during the transfer window.
Shortly before half-time Viduka was booked for a foul on Kola Toure. The Australian international protested his innocence, but referee Mike Riley said the striker had committed a foul with an outstretched arm.
For the second half Middlesbrough sent on substitute James Morrison for Lee Cattermole.
Viduka shot wide and then complained to the referee that Toure had handled the ball before his goalscoring effort.
The game continued to be played at a fast pace with the result in the balance.
Emmanuel Adebayor got the ball in the net for Arsenal but the whistle had gone for offside.
After 61 minutes Arsenal's Swiss international Senderos was sent off for a professional foul on Yakubu and conceded a penalty at the same time. Goalkeeper Lehmann was booked for dissent.
Yakubu showed his usual coolness from the spot by giving Boro the lead.
It was Yakubu's 11th Premier goal of the season and his 13th in all competitions.
Arsenal hit back and levelled the score after 77 minutes through Henry. Following a Lehmann clearance Adebayor headed down for Henry to roll the ball into the net.
Viduka missed a scoring chance when headed over as Middlesbrough hit back.