The City Council’s Zoning Committee on Thursday gave the Lincoln Yards freight train the green light to leave the station after Chairman James Cappleman (46th) tried and failed to run for political cover.

After four hours of debate, the vote was 9 to 4 in favor of the massive mixed-use project that will add 6,000 residential units, create 23,000 jobs and change the face of Chicago’s North Side. Cappleman cast one of the four “no” votes.

Fighting for survival in the April 2 runoff, Cappleman opened the meeting by moving to defer consideration of the $6 billion project.

“A lot of new information has come in recently. And there’s still so much to digest — especially for a project that is this broad,” Cappleman said, his voice almost trembling.

“And so, as acting chair, I will defer these two items.”

At that point, the stunned crowd of protesters gathered in the City Council chambers burst into applause.

Ald. Walter Burnett (27th), one of Mayor Rahm Emanuel’s staunchest City Council supporters, pounced on Cappleman, the Zoning Committee vice-chair occupying the chairman’s hot seat only because disgraced Ald. Danny Solis (25th) was forced to relinquish it.

“They put you here to run the meetings, but you’re not the chairman. … This is not your ward,” Burnett said.

“I move that we vote on this item.”

When Cappleman disagreed, a city attorney argued otherwise. That forced a “vote to vote.” It was was 9-to-4 to go ahead.

A top mayoral aide insisted that Cappleman’s failed retreat was not orchestrated, but Emanuel allies were ready to pounce in the likely event that Cappleman got cold feet.

Others in attendance called it a political charade. Cappleman denied it, but said he told Emanuel before the meeting what he intended to do.

“Have you ever seen this happen before — where a chair deferred something and it was voted otherwise? I imagine you haven’t. I haven’t either,” he said after the meeting.

When debate began, Planning and Development Commissioner David Reifman reiterated the string of concessions that developer Sterling Bay has made to appease area residents.

The number of affordable units on the site of the project that runs along the Chicago River through Lincoln Park and Bucktown has been doubled. Building heights and overall density has been reduced.

A proposed soccer stadium was scrapped. So was the proposed entertainment district. The square footage of a proposed park was doubled. And instead of building two bridges over the Chicago River, Sterling Bay has agreed to build three.

Reifman also made the case for why aldermen should not yield to the demands of both Lori Lightfoot and Toni Preckwinkle to postpone the vote until after a new mayor takes office.

“A site like this is one of the main reasons why Chicago was so competitive in the Amazon bid. These sites are absolutely critical as we consider our fiscal issues and our need to grow our tax base without increasing the burden on existing residents and businesses,” Reifman said.

“Pension funds, insurance companies, institutions and other investors who are the key to solving these issues with us are looking at what we’re doing here today with a site like this and assessing whether Chicago continues to be a good place to invest.”

Before the meeting even began, community activists resorted to political threats, well aware the legislative outcome was pre-ordained.

The Finance Committee still needs to vote to create a new North Side TIF and use $900 million of the proceeds to reimburse Sterling Bay for a host of infrastructure improvements needed to unlock the development potential of the 55-acre site.

“Alderman Cappleman, Alderman [Ray] Lopez, Alderman [Pat] O’Connor, listen to the people of Chicago. Because if you do not delay the vote — if you do not delay the TIF — there will be consequences on April 2,” said Ramirez-Rosa, who easily avoided a runoff by winning 59.4 percent of the vote on Feb. 26.

“People … of Chicago are…tired of a rigged system where big developers give massive campaign contributions and then, they get whatever it is that they want here at City Hall without any concern for the long-term negative impact on the community.”

Marianne Lalonde accused Cappleman, her runoff opponent on April 2, of breaking his promise to demand that Sterling Bay work with the Chicago Housing Authority to “provide more affordable housing for people who earn less than 30 percent of the area median income.” That’s where Cappleman said the “true crisis of affordable housing” exists.

Lalonde noted that a studio apartment in the Lincoln Yards project at 60 percent of the average median income will rent for up to $890-a-month.

“TIF funds should go to benefit the needs of the entire community — not just the wealthy few,” Lalonde said.