Kitson fired home a right-footed shot from 18 yards in the 62nd minute and midfielder Mokoena added a second with 10 minutes remaining as Pompey recorded their fifth consecutive victory.
Joel Ward picked up a knock during Saturday's 2-0 win against Ipswich at Portman Road, so Kanu came in for the only change to Portsmouth's side.
Scunthorpe made five changes to their starting line-up following their 2-0 defeat at Bristol City.
The fit-again David Mirfin replaced the injured Paul Reid in the centre of defence and Eddie Nolan came in for Andrew Wright at right-back.
Baraclough also made three changes in midfield as Michael Raynes, Abdisalam Ibrahim and Michael Collins replaced Sam Togwell, Andy Hughes and Joe Garner.
Portsmouth began brightly but Scunthorpe gradually steadied themselves and in the eighth minute midfielder Mark Duffy made the space to hit a shot just wide.
Moments later Portsmouth created a fine opening which saw former England striker David Nugent advance forward at pace in a marauding run and hit a fierce shot straight at Josh Lillis.
The pendulum swung back in Scunthorpe's favour in the 10th minute when Lee Miller connected with a dangerous cross from Josh Wright which he failed to steer on target.
The Iron's formation of five in midfield began to serve them well and they came close to opening the scoring in the 16th minute.
Miller headed home a cross from Duffy but the score was disallowed after Miller had committed a foul in the build-up.
Portsmouth were then dealt a blow midway through the first half when Hayden Mullins was replaced by Aaron Mokoena because of injury.
Yet the change did not nothing to quell Scunthorpe's momentum as they continued to look comfortable and probe for openings when the opportunities arose.
However, Portsmouth signalled their threat in the 34th minute when Kitson took on Eddie Nolan and found the space to fire goalwards - although the effort was cleared.
In the 37th minute, Duffy cut infield and fired goalwards but Portsmouth goalkeeper was equal to his effort.
Two minutes later Nugent shot wide and shortly before the break Kitson crossed to the back post to Kanu but the veteran Nigerian could only head wide with the goal begging.
The hosts began to dominate and in the 62nd minute Kitson collected possession and struck a right-foot shot into the bottom corner from 18 yards.
Duffy tried his luck for Scunthorpe but Portsmouth survived and then claimed a killer second goal in the 80th minute when Mokoena took a pass from Kanu and fired into the bottom corner with a left-foot shot from 25 yards.
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