The former Pompey winger has joined the south Wales outfit for an undisclosed fee – reported to be £800,000 in a cut-price deal – and signed a three-year deal.
That means that the Blues will receive the £750,000 owed from Wigan in unpaid fees following his move to the DW Stadium last summer.
But Pompey won’t receive a sell-on clause as Lowe leaves the DW Stadium for significantly less than what he joined for.
Lowe moved to the Latics from Fratton Park for in excess of £2m last summer to reunite with ex-Blues manager Paul Cook.
In total, the former Hampton & Richmond ace scored six goals in 48 appearances.
Wigan finished 13th in the Championship but were relegated after being handed a 12-point deduction for entering administration.
The Latics have been cashing in on a number of assets, including Anthonee Robinson and Joe Gelhardt, to help pay debts.
Lowe is the latest to depart as he joins Swansea, who are expected to again push for promotion to the Premier League this season after suffering Championship play-off semi-final defeat to Brentford last month.
Speaking to the Swans’ website, he said: ‘The conversations I’ve had with the gaffer has made a positive impression on me.
‘Also, the stature and size of the club is something you cannot escape.
‘You cannot ignore it, and every time the gaffer spoke to me, he told me the story of what he is looking for and I completely bought into it.
‘He spoke about the hunger of the players, he spoke about what a tight-knit squad there is here, and that is massive for me.
‘Some clubs have not got the right environment for it all to fully flourish, but this sounded like the perfect package and a good fit for me.
‘Earlier in my career I had four years out of the EFL and I was hungry to get back in. I was never going to let the chance go when it came up, and it’s meant I have had to mature quickly.
‘It’s the same with the move here, I will give 100 per cent week in and week out.’