Both sides looked bright before the break, although it was the hosts who led thanks to some inventive play from Lowe.
The Iron were more dominant in the second half, however, and Kevin van Veen grabbed a deserved leveller.
Kenny Jackett made two changes from the side that exited the Checkatrade Trophy earlier in the week.
Top scorer Brett Pitman returned to lead the line, partnered by a fit-again Kal Naismith, who was making his first start for seven weeks.
There was also a system switch, with Oli Hawkins joining Matt Clarke and Christian Burgess in a three-man back-line.
That meant Nathan Thompson advanced into the centre of midfield, where he was joined by Ben Close and recent loan signing Connor Ronan.
Pompey took time to get used to the change in formation and looked a bit shaky at the back in the early stages.
Their opponents almost took advantage, with Luke McGee doing well to deny Tom Hopper and Lowe taking care of the loose ball.
But the hosts were lively at the other end and Ronan was especially bright as he attempted to thread passes through to the front two.
It was LOWE who broke the deadlock on 15 minutes, though, stealing the ball off the foot of Josh Morris and finding the net from a tight angle with a shot that went in off the post.
The Iron were now shaky at the back and it took some desperate blocks to deny both Pitman and Naismith.
And the lead was almost doubled following a fine passing move involving more than half the side, with Pitman drilling a low effort narrowly past the post.
Scunthorpe were providing an attacking threat of their own, although McGee watched Funso Ojo’s attempt sail safely wide.
Their best opportunity to level came when Murray Wallace let fly from outside the box, but McGee was equal to the shot and punched the ball over the bar.
Scunthorpe United 0
And the Iron also had a great chance just after the restart when Hopper cut the ball back for van Veen in the box.
The striker found himself in far too much space, only for Clarke to make a great recovery challenge to deny the visitors.
But there was nothing that Pompey could do to prevent Scunthorpe from drawing level on 53 minutes.
Hopper got free down the left and picked out van Veen in the box, with the Dutchman swivelling and firing home an unstoppable shot.
And it almost got even worse for the Blues, with McGee having to make a fine reaction save from point-blank range to deny Morris.
Pompey tried to make an impression at the other end and Charlie Goode’s slip let in Naismith, only for the defender to recover and make a key block.
Jackett made a double change to try to steady the ship, with Ronan and Dion Donohue making way for Matty Kennedy and Adam May.
That resulted in a change of system to 4-1-4-1, with Naismith and Kennedy out wide and Pitman playing as a lone striker.
And Naismith had a chance to score when Scunthorpe failed to deal with a corner, but saw his angled drive gathered by Rory Watson at the second attempt.
That proved to be the end of the chances, as the final few moments passed by with little goalmouth incident to provide any late drama.
Pompey (3-4-1-2): McGee; Hawkins, Burgess, Clarke; Lowe, Close, Thompson, Donohue (May 71); Ronan (Kennedy 71); Pitman (c), Naismith
Goals: Lowe 15
Booked: Clarke, Hawkins
Subs not used: Bass, Casey, Deslandes, Bennett, Chaplin
Scunthorpe (3-4-1-2): Watson; Goode, Burgess, Wallace (c); Holmes, Bishop, Ojo, Morris; Adelakun; van Veen, Hopper (Novak 84)
Goals: van Veen 53
Booked: Bishop, Adelakun
Subs not used: Kelsey, McArdle, Townsend, Sutton, McGeehan, Toney
Referee: Charles Breakspear
Attendance: 17,741 (386 away fans)