Walsall were seemingly out of their class in the first half but very nearly scrambled to a draw in an attempt to improve their lowly position just two places off the relegation zone.
The Saddlers made a good start with Jorge Leitao setting up Junior but the Brazilian slipped and his weak effort was easily saved by Shaka Hislop.
Danny Sonner then produced a powerful shot for the Saddlers but it was way off target and following these two incidents Pompey took complete control.
Paul Merson produced some neat touches to keep Portsmouth moving forward against a Walsall side which obviously struggled against the division one leaders.
Portsmouth were so much in control that it was no surprise that they steamed ahead in the 14th minute.
In a carnival atmosphere Steve Harper, a former Walsall player, made a run from near the half way line to collect a pass from Steve Stone to score with a shot which stand-in goalkeeper Gavin Ward might well have saved.
Although they were happy to operate in a casual manner Portsmouth appeared to have too much ammunition for a below par Walsall and in the 32nd minute Tim Sherwood produced a long cross from the left and Svetoslav Todorov headed home his 19th goal of the season.
It was all too easy for Portsmouth at this stage but they paid the penalty for taking things too easy when Junior pulled back a goal just before the break.
Portsmouth attempted to retain possession in midfield but Hayden Foxe was caught napping and Junior grabbed the ball to race away unchecked to score with a shot which went in off the post for his 12th goal of the season.
Walsall responded from this lifeline to launch some early second-half attacks with Junior setting up Zigor Aranalde only to see the defender slam his effort into the side-netting.
Merson attempted to restore Portsmouth's domination but the Saddlers went in search of an equaliser as the First Division leaders struggled to regain their early control and lost their composure in the closing stages.
Ward kept Walsall in the game with a fine save from a Todorov drive at a time when a third Portsmouth goal would have settled the match. Only a goalline clearance by Ian Roper prevented Merson capping a good match. Merson beat Ward but Roper never gave up and hooked the ball off the line.