Television evidence indicated goalkeeper Edwin Van der Sar had brought down Jimmy Floyd Hasselbaink outside the penalty area.
The Fulham players protested in vain and Dutch international Boudewijn Zenden piled on the agony by converting the spot kick.
At the final whistle Cottagers boss Chris Coleman advanced 40 yards onto the pitch to remonstrate with Mr Styles but was restrained by several players including Hasselbaink.
The referee and his assistants waited until every player was down the tunnel before they left the field.
Boro must be thankful for the point that still keeps them in with a chance of qualifying for the UEFA Cup next season. But they were far from impressive though and were a poor advertisement for the Premiership
Fulham went ahead after 82 minutes with the first shot on target of the game for either side. It looked at though Brian McBride's goal had given Fulham revenge for a Craven Cottage defeat against Boro until Steve McClaren's side enjoyed a slice of good fortune courtesy of the referee.
In only the seventh minute McBride had a chance to put Fulham ahead but he headed wide of Brad Jones' goal.
Hasselbaink then appealed for a penalty but the referee made the right decision by ignoring the Dutch striker.
Boro skipper Gareth Southgate was booked for a foul on Collins John after 17 minutes but the home side were guilty of numerous misplaced passes as Fulham dominated the first half.
McBride headed another chance wide although he looked in an offside position as Boro fans showed their displeasure.
There was a lack of midfield guile for Boro and their defence looked shaky.
Fulham were unlucky when Luis Boa Morte struck the top of the crossbar with a free-kick. The home crowd tried to rally their team but there was limited response.
Full-back Franck Queudrue cut out a pass and burst through in promising style but his shock was blocked. McClaren made a tactical switch in a bid to lift his team with Zenden moving to the left and Stewart Downing switching into the middle.
But the Boro boss looked a despondent figure in the technical area as his side continued to struggle.
The game was 77 minutes old before Hasselbaink had Boro's best chance when he headed inches past the far post.
Fulham were more enterprising in attack and it looked as though they'd snatched the winner eight minutes from time when Tomasz Radzinski provided the pass and McBride the finish.
Boro fans were streaming for the exit signs but they were stopped in their tracks when Mr Styles gave his highly debatable penalty decision.
The home crowd held their breath before Zenden converted Middlesbrough's first penalty of the season.