The Royals, who narrowly missed out on the play-offs last season, had picked up just five points from their opening five games.
Yet the long trip back home will feel a great deal better after Cox’s neat finish earned an undeserved three points on Teesside.
Middlesbrough headed into the game determined to bounce back from last week’s 3-2 home loss to Sheffield Wednesday, having got back on track with a 3-1 Capital One Cup win over Preston in midweek.
But the poor defending and goalkeeping that plagued Aitor Karanka’s men versus the Owls reared its head again as Cox put the visitors ahead against the run of play.
Middlesbrough enjoyed complete domination thereafter but were left to contemplate another loss after Kike missed glorious chances at the end of either half.
The home side started brightly and showed plenty of ingenuity from set-pieces, Grant Leadbitter pulling a corner to the edge of the box – only to see Adam Clayton volley over.
Reading were caught out again moments later, Leadbitter this time sliding through Kike with a clever free-kick.
The Spaniard drew a save from Adam Federici, who had to be on high alert soon after to turn Albert Adomah’s fizzing effort beyond the post.
And the dramatic start continued as Reading took the lead with their first attack in the seventh minute.
Ryan Edwards was the creator, his inch-perfect ball converted with aplomb by Cox – who looped a delicate volley over Tomas Mejias and into the net.
The game unsurprisingly settled down thereafter as Boro struggled for the same fluency while Reading settled into a rhythm.
Indeed, the next meaningful effort did not come until the 33rd minute, Federici producing a comfortable save to keep out Lee Tomlin’s weak strike.
Middlesbrough did end the half strongly, but Clayton and Kike were both guilty of spurning gilt-edged opportunities.
Picking up where they left off, Karanka’s side continued to pile forward with Tomlin hitting a powerful effort over.
That added to the palpable sense of frustration inside the Riverside, with blatant Reading time-wasting also bringing vitriol from the stands.
Their annoyance was only enhanced, too, when Adam Reach’s cross deflected off Chris Gunter and on to the post.
Still somehow behind, Middlesbrough maintained their endeavour against a side lacking any real desire to press forward.
But, despite bringing on Patrick Bamford – the Chelsea forward who has joined on loan until the New Year – they were finding it increasingly difficult to get past a resolute Royals rearguard.
Even on the one further occasion they did break through, it failed to bring a leveller as Kike somehow turned an effort wide with the goal gaping.