The Blues boss had to rely on his Ivory Coast strikeforce of Didier Drogba and Salomon Kalou to polish off a Pompey side who deserved something from the game.
The African pair scored in either half to condemn Pompey to a fourth straight 2-0 defeat at home in the Premiership against Chelsea.
Mourinho though had to rely on goalkeeper Petr Cech when the score was finely balanced at 1-0, as the Czech Republic international pulled off two inspired saves in the space of two minutes to maintain their slender lead.
Boosted by the return of Ashley Cole after a five-week absence through injury and staring at a 12-point gap at the top of the Premiership, Chelsea began the game with an aggressive looking frontline of three.
It was Portsmouth though who began the stronger, setting the tone for most of the game, as Lomana LuaLua received Kanu's knock down on eight minutes drilling a low shot and forcing Cech into an early save.
Cole then went close for the Blues as Andriy Shevchenko thought he had been fouled on the edge of the penalty area and as the game stopped momentarily, Cole bundled his way past Noe Pamarot, but his attempted chip sailed over the bar.
With that Chelsea began to get a foothold in the game and Shevchenko was guilty of a glaring miss when expertly put through by Robben, but the Ukrainian striker blasted into the stands.
With the initiative firmly behind them the Premiership champions then stole the lead as Cole's searching cross to the far post left Sol Campbell and Djimi Traore confused as to who was marking Drogba.
The Ivorian pulled away to give himself enough space to dispatch a perfectly-timed shot into the corner of the net from an acute angle.
Matthew Taylor then wasted two golden opportunities to claw Portsmouth back into the game.
O'Neil's clipped ball found the midfielder in space and through on goal, but his heavy touch took him too far away to set up a shooting opportunity.
O'Neil was provider again when he flicked on Pamarot's cross and this time Taylor's touch deserted him again as he swung with his right foot from eight yards, but missed the ball completely.
The second half was barely two minutes old when the lively Arjen Robben exchanged passes with Drogba before scraping the face of the crossbar.
Chasing a maiden win in the Premiership against Chelsea, Pompey then went on the offensive forcing Cech to pull off his match winning saves, first from substitute Andy Cole and then Kanu.
The stop from Cole was the most impressive as he dived away from the flight of the ball, but doubled his body back to keep out the former Manchester United striker.
Despite being on the ropes, Chelsea then killed the game off as Lampard's long ball was headed on by Cole and Kalou, on as a late substitute, nipped in between Pamarot and Linvoy Primus to finish well.