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."

Harry Davis gave the visitors a shock lead before goals from Mikael Lustig, Scott Sinclair, Moussa Dembele and Leigh Griffiths saw Celtic home.
"St Mirren are at the bottom of the Championship, but they are the best team we have played domestically," Rodgers said.
"They are well organised."
Celtic trailed 1-0 at the break and could have been 2-0 down early in the second half when Moussa Dembele's mishit clearance rebounded off his own crossbar.
"I wasn't worried at half-time, but I knew we hadn't played as well as we could have," the Celtic manager told BBC Scotland. "Second half, we just had to stay calm and up the tempo a bit.
"Once we got the first goal we really opened up and we end up getting four goals in the second half.
"I think what was very good today was that again it was another good demonstration of the players under pressure. The players and the supporters stayed calm, stayed behind the team and that's what you have to do. We had a great second half but we'll learn from the first half."
St Mirren manager Jack Ross was proud of his side's display and felt the final score was not an accurate reflection of the match.
"We understood how we had to play and we did that in the first half," Ross said. "But, once they get that momentum in the game, Celtic are difficult to stop.
"They recognised they had to do something different and they brought on Leigh Griffiths.
"I don't think my players deserved that scoreline. The focus is now on the next game and it would be a bigger achievement to escape relegation than if we had won here today."
Rodgers, who confirmed goalkeeper Craig Gordon should complete the "formalities" on a new contract with the club next week, is relishing taking his team back to Hampden for the cup semi-final.
"I'm really looking forward to going back to Hampden again. We've been there twice for the League Cup, semi-final and final, and the team were magnificent in the games.
"We just wanted to get there and we got there so that's the most important thing."
Carwyn Jones met Leanne Wood to discuss Brexit on Thursday, after their parties clashed over the Welsh Government's response to the EU referendum.
[NEXT_CONCEPT]
Brendan Rodgers was full of praise for St Mirren after Celtic were forced to rally from a goal down to make the last four of the Scottish Cup.