The Australian, signed from Leeds in the summer, thought he had scored the all-important goal when he bundled home, but was adjudged to have fouled Portsmouth goalkeeper Jamie Ashdown.
Steve Cotterill's side could have nicked it late on but Luke Varney saw his shot rebound off the post.
In a game of few chances, both sides failed to build on their first victories of the season in midweek.
Albert Adomah, after neat work with Marvin Elliott, had the opening chance of the match but Jamie Ashdown was equal to the midfielder's 20-yard effort.
City, unchanged from the midweek win at promotion-favourites Leicester, had the better of the opening exchanges, with Jamal Campbell-Ryce looking lively, but failed to convert possession into chances.
Portsmouth, lacking an attacking threat early on, finally came to life after 17 minutes but Greg Halford saw his 30-yard shot fly over the bar.
The visitors started to apply the pressure and, after David Norris and Hayden Mullins linked up, the former saw his 20-yard strike well blocked by James Wilson.
Dave Kitson, fresh from scoring the winner in Tuesday's 1-0 victory over Reading, headed over from Liam Lawrence's teasing cross in the closing stages of the opening half.
Portsmouth started where they left off in the first half and, after good work from Kanu, Kitson saw his shot blocked by Jordan Spence.
Lawrence tested Dean Gerken from 25 yards, before the hosts went up the other end and saw Kilkenny almost open the scoring with a 20-yard effort that whistled past the post.
With defences on top in the opening half, the game started to open up and Lawrence should have done better when he headed straight at Gerken, who did well to punch the ball to safety.
Campbell-Ryce was denied by Ashdown before Kilkenny found the net after 65 minutes but the midfielder was adjudged to have impeded goalkeeper Ashdown.
Pompey responded and, on 72 minutes, Varney was unlucky not to net his first goal for the club when he saw his curling shot from the edge of the box rebound off the post.
The mis-firing Kitson wasted another chance, this time firing over from six yards, while Martyn Woolford, coming on as a substitute, was released by Nicky Maynard but, after the former Scunthorpe winger cut back inside, fired straight at Ashdown.
Benjani, introduced for Kanu in the second half, had a chance late on but headed Hayden Mullins' cross over the bar from 12 yards as both sides took a share of the spoils.
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