Dunne, Wallace and Barcham on target at Fratton Park
Wallace drilled a shot narrowly wide at the other end as Pompey tried to apply some pressure on their opponents.
The game quickly descended into a scrappy affair, however, with both sides struggling to keep possession.
Agyemang looked lively in the opening stages, although Wallace could not quite bring his pass under control after four minutes.
And there were also returns for Joe Devera and Dan Butler as the Blues switched to a 3-5-2 formation.
Patrick Agyemang was handed his first start of the season alongside Craig Westcarr up front.
Andy Awford made three changes from the side beaten at Southend on Saturday.
And substitute Andy Barcham netted from close range in the final seconds to add a gloss to the scoreline.
Andre Boucaud then saw red for a second bookable offence before Jed Wallace secured victory from the spot after Paul Robinson had been fouled.
James Dunne lit up a dire first half by breaking the deadlock with a rocket of a shot.
Pompey returned to winning ways with a comfortable 3-0 victory over 10-man Dagenham & Redbridge.
Pompey 1 Dagenham & Redbridge 0 Half Time:
The visitors then almost denied them an interval lead when, in stoppage-time, Ashley Chambers’ 30-yard rocket crashed against the crossbar.
But Pompey were ahead moments later as Agyemang teed-up DUNNE, who sent an unstoppable shot thundering into the net.
Fortunately for the centre-back, however, goalkeeper Mark Cousins quickly adjusted his feet to keep the ball out of the net.
Brian Saah stuck out a foot to try to intercept Alex Wynter’s weak effort, but only succeeded in turning it goalwards.
In fact, it was a Dagenham player who had the Blues’ first decent opportunity on 39 minutes.
It failed to ignite the match, though, which continued to meander along with little action to excite the crowd.
Boucaud, who had already been booked before the break, went in late on Agyemang and was shown a second yellow – and subsequent red – by referee Carl Berry.
But the visitors’ task was made a lot harder when they were reduced to 10 men on 62 minutes.
Jack Whatmough could then only clear Nathan Green’s cross as far as Jamie Cureton, who blazed wildly over from inside the box.
Daggers skipper Abu Ogogo tried to draw his side level early in the second half, but was unable to beat Jones from distance.
Matt Partridge bundled Robinson over in the box as the defender went up for a corner and WALLACE stepped up to send Cousins the wrong way from 12 yards.
And Pompey soon made their numerical advantage count by doubling the lead from the penalty spot.
Awford immediately decided to wrap Agyemang up in cotton wool, with the striker receiving a standing ovation as he made way for Miles Storey.
The replacement thought he had scored on 80 minutes, but was adjudged to have been in an offside position as he converted Craig Westcarr’s cross.
Jones; Devera, Robinson, Whatmough; Wynter, Dunne (Close 86), Wallace, Hollands (c), Butler; Westcarr (Barcham 90+2), Agyemang (Storey 73) Pompey (3-5-2):
BARCHAM did add a third in stoppage-time when, just seconds after entering the fray, he converted Wallace's low cross from close range
Dunne 40, Wallace 69 (pen), Barcham 90+2 Goals: 13,648 (144 away fans)Attendance:
Carl Berry Referee:
O’Brien, Gayle, Connors, Goldberg Subs not used:
Boucaud (two yellow cards) Sent off:
Cousins; Batt, Partridge, Saah, Green; Boucaud; Porter, Howell (Labadie 80), Ogogo (c), Chambers (Yusuff 77); Cureton (Hemmings 77) Dagenham & Redbridge (4-1-4-1):
Poke, Webster, Ertl, Maloney Subs not used:
Hollands, Westcarr, Butler Booked: