But the 29-year-old scored just before half-time before a Danny Murphy penalty and Clint Dempsey's calm finish sealed a fine victory.
Fulham are now up to eighth in the Premier League, but Gareth Southgate's visitors are winless in six games and the only impact they made on this game was on Andy Johnson's shin as Julio Arca launched into a disgracefully high challenge that should have brought a straight red card.
The margin of defeat could have been even worse as Middlesbrough appeared to give up the ghost in the second half, with former Boro goalkeeper Mark Schwarzer never truly tested.
The game started at a snail's pace, with neither side confident either on the ball or going forward.
It was clear that the first goal was going to be particularly crucial and both sides missed good chances to claim it as, firstly, John Paintsil somehow headed wide from four yards out for the hosts before Sanli Tuncay's flick skimmed the post for Middlesbrough.
But it was to be Bullard who stepped up to the plate for Fulham.
All the talk recently has been of the £5million-rated player leaving for pastures new but that appears unlikely while he is scoring goals, as he has done in his last two home games.
It was a horrible goal to give away as Chris Riggott was turned far too easily by Bobby Zamora and when Ross Turnbull spilled the tame shot, Bullard ran past two static defenders to net the rebound.
That came shortly after Arca had left his mark on Johnson with a raking challenge that started at shin height and ended with his studs embedded in the striker's ankle - a tackle for which a yellow card was hardly sufficient punishment.
But retribution was swift and this time it was Middlesbrough who were left feeling aggrieved.
There appeared no danger as Tony McMahon went to clear but after Zamora blocked his shot, the ball hit his arm.
Intent was certainly minimal but that made no difference as referee Keith Stroud, on the advice of his assistant, pointed to the spot.
Murphy calmly slid the ball into the far corner for his fourth of the season and it was the Fulham captain at the heart of the third goal just before the hour-mark as he slid the ball across the box to the criminally unmarked Dempsey, who took his time before placing his shot across Turnbull and inside the far post.
Fulham played out time in extreme comfort as they extended their impressive defensive record to just 12 goals conceded in 17 league games - a statistic Middlesbrough could only dream of on this evidence.