DUP MP Ian Paisley revealed his party would support Labour during the debate.
Later this evening Labour pushed through another motion on blocking the £250 rise in tuition fees - but again it did not go to an official vote.
The party's MPs will vote with Labour in favour of a "fair pay rise" for NHS workers and against the government's rise in tuition fees - the first time they will have broken with the Conservatives since their deal after the election.
The DUP's stance would leave the Government facing defeat on both issues, although Tory MPs are expected to abstain from the votes because they are non-binding.
"We welcome the Prime Minister's commitment to flexibility on the pay cap".
Because the motion was not binding it would not have amounted to a breach of the £1 billion Tory/DUP deal.
Under the "confidence and supply" deal, the DUP agreed to back the Conservatives only on finance bills, Brexit legislation and protecting "national security".
"Maybe the House will agree that the points that have been raised today are such that we should send out a clarion call from this House that we do agree with the points that have been raised, all across this chamber today".
Political Correspondent John Manley
"Lifting the cap on nurses' pay and in the public sector generally is our party policy".
She said: "We have a constitutional crisis because this Government is running scared and not allowing votes in this House".
"We made it very clear to her Majesty's government on issues like this we reserve the right to vote on the basis of our own manifesto".
As surprised MPs took in the decision, Shadow Health Secretary Jonathan Ashworth said: "Is it not clear that the House has been unanimous in saying we should end the pay cap in the NHS?"
Ms Rayner said ahead of the Opposition Day vote: "This latest tuition fee rise could cost students up to a thousand pounds more over a university course, yet they are refusing to keep their promise to graduates that the repayment level would go up with inflation".
On Tuesday, Downing Street confirmed the one percent limit on public sector pay rises is to be scrapped.
During the debate Health Secretary Jeremy Hunt labelled the Labour motion as "bogus" and said it was "absolute nonsense" to suggest the cap over the last seven years was part of an "ideological mission" to reduce the size of the state.
Barack Obama to host two-day global summit in Chicago
President Barack Obama speaks during his farewell address at McCormick Place in Chicago, Tuesday, Jan. 10, 2017. The summit will be the beginning of several activities the foundation is planning, Obama said.
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