The Hatters confirmed the striker’s arrival soon after County had confirmed the 25-year-old’s departure from Meadow Lane.
The Magpies confirmed Wootton had ‘joined an EFL club’ ahead of the summer transfer window officially opening on Friday.
Now it’s been announced that he will play for Stockport following their return to the Football League.
Welcoming the former Scunthorpe front man to Edgeley Park, Stockport manager Dave Challinor said: ‘I’m absolutely thrilled that Kyle has agreed to join us and be part of what we are trying to achieve at the club.
‘His profile as a player and his age are perfect for us.
‘We feel as a team that we will play to his strengths, he will get opportunities to score and his record shows he can finish; but also having spoken to him both he, and we, feel that he can improve and really grow with us.
‘He’s been a long-term target for us, so to get this one over the line is brilliant and will undoubtedly strengthen us and complement the strikers we already have at the club.
‘I’m really excited to start working with him and I’m sure he will fit into our group seamlessly and become a favourite at Edgeley Park.’
Pompey appeared to be in a strong position in the race to land the forward, with the former Scunthorpe man understood to be keen on a move to PO4.
However, the Blues were dealt a blow in their pursuit of Wootton this week when Stockport emerged as the front-runners.
Reports claimed the newly-promoted EFL outfit were prepared to offer the striker a £5,000 per week deal to move to Edgeley Park.
Blues boss Danny Cowley has admitted he would like to add four new additions up front this summer, with Kyle Joseph, Kion Etete, Aaron Collins, George Hirst, Morgan Whittaker, Danny Hylton and Brandon Thomas-Asante all linked so far, alongside Wootton.