The first minister's spokesman said "differences remain". The two leaders agreed to hold further talks.
The meeting came after Labour AMs voted against a Plaid Cymru assembly motion to support "full membership" of the EU's single market.
Labour had sided with UKIP and the Tories in the vote on Wednesday night.
Plaid said the move by Labour amounted to support for a so-called "hard Brexit".
But Mr Jones said he had consistently called for the UK to retain "access" to the market since the referendum result.
The two parties are already involved in discussions over the budget, powers for the assembly and legislation - part of a deal allowing Labour to regain power after May's election.
But there have been angry exchanges between their parties since Wales voted to Leave, with Plaid accusing the first minister of changing his position on what should happen next.
The single market is Europe's tariff-free trading area.
Mr Jones and Ms Wood campaigned side-by-side for a Remain vote in June's referendum.
The first minister's spokesman said: "Differences remain between the two leaders and their respective parties, but both have agreed to discuss further the challenges Wales faces."
Carwyn Jones met Leanne Wood to discuss Brexit on Thursday, after their parties clashed over the Welsh Government's response to the EU referendum.