The Imps boss believes his side’s 2-1 reverse was preventable, with defensive errors leading to their downfall as they lost in the league for the first time since the opening day.
Kennedy worked with Clarke at Ipswich, before he made his move to Pompey in 2015 and started his rise to becoming a £4m player.
The former Liverpool man told how the defender went through a similar period of making different errors, which helped him become a better footballer.
That is the learning he thinks Lincoln have to take from their Fratton reverse.
He told Lincoln’s YouTube channel: ‘The only thing which gives me heart about the mistakes is it’s different people.
‘If it was the same people making the same mistakes and you keep playing them, there’s clearly a problem with the head coach. If it’s different mistakes…
‘I remember Matt Clarke at Ipswich. Matt got a multimillion pound move to Brighton and has probably played 200 games.
‘I remember every week at Ipswich in the 23s Clarkey gave away a goal every week - but it was different.
‘I just said to him as long as he learns from each individual one he’ll get better - and he’s had an outstanding career.
‘That’s also the environment we have at Lincoln as well - it’s just a tougher platform.’
Lincoln almost snared a leveller in stoppage time, as Will Norris came to Pompey’s rescue with a key point-blank stop to deny Paudie O’Connor with Adam Jackson firing the follow-up over.
Kennedy added: ‘It looked like it got cleared off the line.
‘It’s so ironic, because we brought Jacko on here at the end last year and he had an unbelievable chance to score with a header.
‘But I thought Jacko was awesome today, he was absolutely awesome.
‘It sums him up, because you could see his disappointment on the pitch.
‘He had his head in his hands after the game, but we don’t put him in the team to score goals, so there’s no criticism on that - it’s a difficult technical action.’