Di Natale missed almost two months of the campaign with a knee problem before making his comeback in mid-January against Parma.
But after a scoreless encounter at home to struggling Como, Baldini conceded Di Natale was still striving for peak fitness.
"Di Natale? He isn't at the top of his form because he missed about 50 training sessions," said Baldini.
"But I have to thank my players who still try to achieve good results."
In a scrappy tussle at Stadio Carlo Castellani, which was characterised by a string of mistakes from both sides, Baldini was happy to take a point.
He added: "In the second half we had many difficulties but luckily we've obtained a positive result.
"When there are problems like ours, the important thing is not losing. We played better in the first half."
