John McDonnell was forced to defend the shadow home secretary despite her giving a speech in Westminster Hall three hours before the vote.
She also sent out a tweet criticising Theresa May’s “shared society” less than an hour before MPs were due to vote.
Speaking on Radio 4’s Today programme, Mr McDonnell was grilled by host Nick Robinson.
Robinson asked: “How is she feeling by the way? Because apparently, she wasn’t quite well enough to come to the Commons yesterday.”
Nick Robinson probed John McDonnell over Diane Abbott's absence from the House of Commons
How is she feeling by the way? Because apparently she wasn’t quite well enough to come to the Commons yesterday
The Labour MP replied: “She wasn’t very well, there wasn’t going to be a close vote – if there was a close vote they would bring in even sick people, but she wasn’t very well so she wasn’t in attendance.”
The radio presenter probed further and asked if the politician had spoken to Ms Abbott, to which he replied: “Not this morning no, to be honest with you.”
Robinson then asked: “Is it Brexit flu? Some people are wondering.”
However, Mr McDonnell reiterated: “No I don’t think so. I think she’s not very well, we’ve all been down with various bugs over the last few weeks.”
Government Loses Brexit Vote Appeal
Tue, January 24, 2017
Britain's most senior judges ruled that Prime Minister Theresa May does not have the power to trigger the formal process Article 50 for the UK's exit from the European Union without Parliament having a say.
1 of 12
Issued by the Supreme Court of (top row, from the left) Lord Neuberger, Lord Mance, Lord Kerr, Lord Sumption, (bottom row, from the left) Lady Hale, Lord Clarke, Lord Wilson and Lord Hodge, who agreed with the majority decision that the Government could not trigger Article 50 without Parliamentary approval.
Refusing to let the topic slide, the host pushed further and asked: “So she’s not made to feel a bit sick by a position she’s uncomfortable with?”
The Hayes and Harlington MP said his whole party was "uncomfortable" but insisted the Labour Party was comprised of “democrats".
“Look, we’re all uncomfortable with the position,” he said. “We campaigned for Remain but we’re democrats, we have to accept the will of the people.”
The awkward exchange comes after 47 Labour MPs defied Jeremy Corbyn’s three-line whip and voted against Article 50.
Defending Mr Corbyn's decision to impose the whip on the radio station last week, Ms Abbot said it would be “wrong” to vote against triggering Article 50.
Ms Abbott added: “How could MPs vote in a referendum and turn around and say ‘it went the wrong way so we’re ignoring it’? There’s a real democratic principle here and the vote on Wednesday begins the process.
“It’s not the beginning and the end but of course it’s a challenging situation for Labour.”