The Shadow Chancellor described the list of priority issues that will be debated – which excludes EU withdrawal – as “democracy at work”, because it was decided by delegates in Brighton.
Labour campaigners for permanent membership of the EU single market were furious after they were denied an attempt to shift party policy.
One, former shadow Cabinet member Heidi Alexander, branded her own party “a laughing stock” for ignoring the biggest political issue of the day.
But Mr McDonnell insisted the conference would talk about Brexit – although there will not be a vote on long-term single market policy, after a transition period.
And he said: “In our new politics, we are saying conference needs to be controlled by the delegates. They decide what we will debate, not the leadership. This is democracy at work.”
The row has sparked a warning from Labour’s elections chief that divisions over Brexit could tear the party apart in the months to come.
Mr McDonnell has said it is “difficult to see” how Britain could stay in the single market because of “exploitative” freedom of movement rules that allow employers to undercut wages.
However, in interviews ahead of his conference speech today, the Shadow Chancellor insisted he was working to achieve a united Labour policy – and quickly.
“We are building that answer now, but we have got to build a consensus,” he said.
“We can’t be in a situation where we are trying to impose a solution on the British people. We have to build a compromise in the traditional British way.”
That effort included talks with other left-wing European parties, which also wanted reform of freedom of movement, Mr McDonnell said.
The shadow Chancellor has said Labour would be in favour of maintaining membership of a “changed single…