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The Chelsea head coach could not hide his emotion towards his new forward as he whispered in his ear in the 67th minute at Stamford Bridge on Saturday.
Palmer had coolly opened the scoring from the penalty spot and, as the focal point of the Chelsea attack, had several times come close to a second goal.
He played out of position as a false nine, amid injury concerns around strikers Nicolas Jackson and Armando Broja.
Cole Palmer played as a false nine against Arsenal
Palmer has now started four consecutive matches in all competitions and helped Chelsea record three wins and Saturday's draw.
Pochettino has described him as a "link player" and he has brought composure to an attack that was regarded as the most wasteful in the division.
His confidence, ability and winning mentality was built under Pep Guardiola at Manchester City and is allowing him to fit seamlessly into Pochettino's plan.
Such has been his impact, his PS40million move from Manchester City is beginning to look like a bargain.
Two goals and two assists mean Palmer now has four goal involvements this season. That is despite initially missing four matches after joining on transfer deadline day.
Stand-in Chelsea captain Conor Gallagher said of Palmer: "As soon as he came into Chelsea, you could see his talent in training and now he's showing it in games. He's helped us massively since coming in."
Despite an impressive display from Palmer, and even after Mykhailo Mudryk made it 2-0 early in the second half, Chelsea's late collapse leaves them in 10th place.
There was a sense of frustration after the match as Robert Sanchez's mistake playing out from the back gave Arsenal a lifeline through Declan Rice's first-time shot.
Leandro Trossard completed the comeback by tapping in Bukayo Saka's cross.
Pochettino refused to blame individuals, pointing instead to general poor decision-making late on and tiredness in his midfield.
Enzo Fernandez and Moises Caicedo helped dominate midfield for 75 minutes but faded after playing through jet lag after they had returned from South America last week.
Mistakes can be attributed to youth but also the recent injury crisis at Chelsea, which left substitutes like returning captain Reece James rusty and unable to make his usual impact.
Once the dust settles on the Arsenal draw, Chelsea will realise they can compete with England's best teams once again, ahead of a run coming up that includes games against Tottenham, Manchester City, Newcastle and Manchester United.
Palmer is ready to be the star forward, having already become their main penalty-taker.
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