The 20-year-old cut inside Georges Santos before firing inside the far post, but ten minutes later he missed a similar chance, firing over the bar from Paul Merson's pass.
Pompey dominated the rest of the first half. A Merson free-kick curled narrowly wide of Danny Coyne's goal on 31 minutes and five minutes later debutant Tim Sherwood had an eight-yard shot deflected over the bar.
Harry Redknapp's side continued to dominate after the break, but did not score their second until Grimsby defender Simon Ford put past his own goalkeeper on 74 minutes.
Portsmouth goalkeeper Shaka Hislop was only tested once when Darren Mansaram's 83rd minute header forced him to concede a corner.
Portsmouth manager Harry Redknapp said: "Yakubu showed what pace he had but we needed that second goal because if they had scored it would have changed the game.
"We needed this win and I'm delighted.
"I was pleased with Tim Sherwood as well. He is going to be a very useful player for us as we approach the end of the season. He hardly ever gave the ball away."