Karanka masterminded a perfect September as Boro won all four Championship games, achieving a 10-2 goal differential and ending with an impressive 3-0 victory over Leeds United.
He said: "It's amazing for me. I've been a manager here for two years and we have this award again.
"It's not about me, it's about the staff, the players, the people at the club, and the supporters. Without them all it would be impossible.
"September was a good month for us, winning those games, but we have to keep going in the same way and keep working."
George Burley, who chairs the Sky Bet Manager of the Month judging panel, added: "After the disappointment of losing the Sky Bet Championship Play-Off Final last season, Aitor has kept the momentum of his side moving forward.
"They have had a great month winning all four games and are looking like a side which is capable of going a stage further this season."
Sky Sports' Football League pundit Don Goodman said: "Karanka's Boro have coped with the pressure of being favourites for promotion and have finished the month just two points behind leaders Brighton.
"He will be hoping the team can carry on this form into October and beyond as they mount a title challenge."
Sky Bet Football Trading Manager Paul Lowery said: "Karanka's Boro went perfect in the month of September, scoring multiple goals in each of their victories.
"The Spaniard recently reached 100 games at Boro and has impressively won more than half of those matches.
"Opening the season as 9/2 favourites, Karanka and his squad have been business-like in working their way up the table and enjoy one of the best defensive records in the league.
"We make them 13/8 to have overtaken Brighton as league leaders by the end of October."
In Sky Bet League 1, former Boro star Jimmy Floyd Hasselbaink of Burton Albion was named Manager of the Month. Accrington Stanley manager John Coleman won the League 2 award.