Goals from James Coppinger and John Marquis twice saw Rovers lead only for Anton Walkes and Brett Pitman to draw the hosts level.
Portsmouth finished the game with nine men after goalkeeper Stephen Henderson was forced off injured after all substitutions had been made and Christian Burgess was sent off in added time.
Darren Ferguson showed little hesitation in throwing his two new signings in at the deep end as he handed starts to Andy Boyle and Tom Anderson.
The introduction of the newcomers were two of three changes from the defeat to Bristol Rovers with Jordan Houghton also returning to the side.
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Out went the injured Joe Wright while Rodney Kongolo and Craig Alcock dropped to the bench where Luke McCullough and Alex Kiwomya made their first appearances of the season.
Rovers started with a good tempo, pressing Portsmouth hard to enjoy the better of the opening stages.
And they made it count just four minutes in as they took the lead.
Coppinger won the ball in midfield and carried to the edge of the box where he slid in Alfie Beestin who was tackled only for the veteran to dart in and slot under Portsmouth keeper Stephen Henderson.
Rovers enjoyed plenty of success in the opposition half, closing down space incredibly well to leave Portsmouth struggling to get over the half way line.
Coppinger in particular was thriving as he roamed largely untracked in front of the Portsmouth defence.
He drilled a fine effort from 25 yards which Henderson had to stretch to claim out of the air.
And he drew a fingertip save from the Portsmouth keeper when lashing a low effort off a Beestin knockdown from a Tyler Garratt cross.
Coppinger was afforded all the time in the world to clip an excellent ball over the top which John Marquis deftly headed past Henderson only for the offside flag to go up.
Portsmouth came to life after the 15 minute mark and Christian Burgess drew a decent save from Ian Lawlor when he attempted to poke in from a Ben Close free kick.
But the hosts somehow found themselves level by the 19th minute.
A corner sparked a scramble in the box but Pompey debutant Walkes drilled into the roof of the net from close range.
From the equaliser, the hosts wrestled control of the game and quickly pushed for a second.
Oliver Hawkins should have headed them in front after shaking off Boyle to meet a Matty Kennedy cross but sent his effort well wide.
And Lawlor produced a fine reaction save on his post to keep out a Matt Clarke header.
Portsmouth continued to push without truly threatening Lawlor over the final 15 minutes of the half. But Rovers were largely penned into their own territory.
The half would finish with a good dose of controversy when full back Dion Donohue left the ground to jump into a challenge on Matty Blair on the touchline.
Referee Graham Salisbury reached for his back pocket as he walked over. Marquis charged in, closely followed by Christian Burgess who bundled into the striker, sparking a pushing match.
After a lengthy delay, Salisbury showed a yellow card to Donohue, who could count himself somewhat fortunate.
The second half was a much more even affair with both sides struggling to create clear cut chances.
Portsmouth threatened when Ben Close was sent through on goal but Lawlor raced out to block his shot.
With the hosts threatening to take control again, Ferguson sent on Kiwomya and McCullough for their first appearances of the season, switching to a 3-5-2.
And just after the hour mark, Rovers went back in front when Marquis stooped to meet a Coppinger corner with a header into the bottom corner.
Portsmouth pushed for the equaliser and it took a fine save from Lawlor to keep out an awkward effort from distance from substitute Naismith.
But from the subsequent corner they were level. Donohue's cross dropped at the far post and substitute Pitman bundled in from close range.
There was time for a late twist when Pompey keeper Henderson was forced off injured after they had used all their substitutes. It left the hosts down to ten men and with Naismith deputising in goal.
The situation got worse for the hosts when Burgess saw red for a second yellow card as the game ticked into added time.
Rovers pushed hard but struggled for real opportunities and stand-in keeper Naismith saved with his legs from Whiteman on the line in their last opportunity.
Portsmouth: Henderson, Walkes, Burgess, Clarke, Donohue, Thompson, Close, Evans (Naismith 72), Ronan, Kennedy (Lowe 72), Hawkins (Pitman 59). Subs not used: McGee, Chaplin, Deslandes, Widdrington.
Rovers: Lawlor, Blair, Boyle, Anderson, Garratt (McCullough 59), Houghton, Whiteman, Rowe, Coppinger (Kongolo 73), Beestin (Kiwomya 59), Marquis. Subs not used: Marosi, Alcock, Mason, May.
Referee: Graham Salisbury (Lancashire)
Attendance: 17,364 (366 away)