The 42-year-old Spaniard did not take training on Saturday and assistant Steve Agnew was in charge for Sunday's 2-0 defeat at Charlton.
Karanka was thought to be considering his future at the Championship club.
But a Middlesbrough statement on Monday said he "will be resuming first-team duties with the club with immediate effect".
It added: "We have 10 games left this season and as a club we are fully focussed on what remains of our Championship campaign."
Karanka took charge at the Riverside in November 2013.
His Middlesbrough side were top of the table by six points on 12 January, but they are now seven points behind leaders Burnley.
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Middlesbrough boss Aitor Karanka is to stay at the club after walking out of training following a row last week.