The 26-year-old has scored once since his big-money move to Teesside.
Rhodes, a £9 million (The Mirror) January signing from Blackburn Rovers, was given the nod by Boro boss Aitor Karanka to lead the line, but the 26-year-old was withdrawn with 20 minutes to go after struggling to impress.
His replacement, David Nugent, went on to flick home a 91st-minute winner at the Riverside as Karanka's boys reclaimed second spot in the Championship, with a two-point cushion over Brighton & Hove Albion in third.
Rhodes has still just netted once in 10 Championship appearances - six of which have been starts - and Stone believes that a lack of confidence is a big reason behind the underwhelming form.
"Jordan Rhodes's runs off the ball have been very good," the Nottingham Forest legend said on BBC. "He looks like he's just lacking in a bit of confidence but his work-rate has been fine.
"I would have said they could have gone with two up front at this stage but Aitor Karanka will not change from his system. It's his team and they've been successful doing it that way."
He might be presently struggling for goals, but Rhodes, who netted 10 of them this season before his move to Teesside, clearly has the pedigree to help fire Boro into the Premier League.
They sit well placed to move into the big time, with just four points now separating them from league leaders Burnley.