The 82-year-old left-winger, who has been in the Commons since 1970, lost his place on the NEC to former minister John Healey in a ballot of the Parliamentary Labour Party, sparking heavy criticism from some supporters.
Jim Murphy, the East Renfrewshire MP and shadow international development secretary, wrote on Twitter: "Really sorry to hear that Dennis Skinner was voted off Labour's NEC", adding: "A brilliant MP & good friend. Hopefully he'll make NEC comeback."
Paisley & Renfrewshire North MP Jim Sheridan tweeted: "Have lost a powerful voice for the working classes at the heart of the Party. A sad day for Labour."
Shadow cabinet office minister and NEC member Jon Ashworth posted: "So sorry that Dennis Skinner (who I voted for) not re-elected. He will be a big loss."
MP John Mann said the vote showed "naive political immaturity in [the] Parliamentary Labour Party in knocking Dennis Skinner off NEC in election year."
Labour leader Ed Miliband's office dismissed suggestions that Mr Skinner had been the victim of an organised campaign by the leadership.