Stevenage 2 Pompey 1
Gavin Mahon was sent off as Pompey’s FA Cup campaign was halted at the first hurdle for the fourth season in succession.
Stevenage had already looked out of reach as two goals from Francois Zoko gave the League One side a comfortable half-time lead.
But Mahon was given his marching orders after catching Filipe Morais with his elbow early in the second half and that looked to have ended the contest.
Substitute David Connolly managed to restore hope with a close range finish, but the Blues were unable to stage a comeback.
Guy Whittingham made three changes from the side that beat Exeter in the league the previous week.
Skipper Johnny Ertl was partnered with Mahon in the centre of midfield, while Andy Barcham started wide on the left.
Pompey attacked straight from kick-off and Jed Wallace saw a shot strike the post after just 58 seconds.
But it was Boro who broke the deadlock on eight minutes, despite Trevor Carson making a fine save to deny Morais.
A melee in the Blues box followed before Zoko was able to keep his composure and poke the ball home.
Stevenage continued to cause problems and went close with a clever free-kick routine before Luke Freeman saw his effort blocked.
But the visitors almost grabbed a shock equaliser on 19 minutes. Barcham’s deflected shot was just about punched clear by Chris Day and Patrick Agyemang could only scuff the loose ball wide.
Agyemang then collected Wallace’s pass, but was crowded out as he attempted to turn and shoot inside the area.
The hosts were still looking dangerous themselves, however, and Carson had to be at his best to keep out Zoko’s fierce 20-yard drive on 27 minutes.
It was certainly proving to be open cup clash and Barcham was next to go close, narrowly clearing the crossbar after being fed by Agyemang.
The winger then had appeals for a penalty turned down before Wallace volleyed over from the right hand side of the Boro box.
Stevenage were looking more potent in front of goal and took the chance to double their advantage on 38 minutes.
It was a fine effort from Zoko, who collected Lucas Akins’ pas and showed some nifty footwork to work his way through the Blues back-line and slam the ball home.
Day was forced into action late in the half to keep out Mahon’s drive from distance, but the Blues went in two goals down at the break.
Half Time: Stevenage 2 Pompey 0
Whittingham made a double switch at the start of the second half with Connolly and Danny East replacing Agyemang and Yassin Moutaouakil.
It was still Stevenage looking more threatening, though, and Bruno Andrade dragged a shot wide after Carson weakly punched Morais’ cross.
And Pompey’s hopes of progressing were all but over on 50 minutes when Mahon's elbow struck Morais and referee Gary Sutton pulled out a red card.
They came close to reducing the deficit moments later, though, with Barcham unable to make a clean connection with Ryan Bird’s cross at the far post.
But Stevenage were keen to make their numerical advantage count and Akins forced a save from Carson after Ertl had lost possession.
Pompey fans were still making a racket in the away end, but there were no signs of their side getting back into the tie.
Then, all of a sudden, the Blues broke quickly up field and were able to reduce the deficit.
It was great work by Barcham who surged up the pitch and burst into the box before seeing his shot saved by Day.
The keeper could not get the ball to safety, though, and Bird got a slight touch before CONNOLLY bundled it over the line.
Stevenage should have restored their two-goal lead on 77 minutes, but Zoko glanced Freeman’s header wide from just a few yards out.
But Pompey were certainly not out of it and Connolly sent a fine cross into the box that Bird was unable to make a clean connection with.
It was end-to-end stuff now and Morais burst through on goal before curling a shot inches past the post.
Barcham was looking dangerous at the other end and had his second penalty appeal of the afternoon turned down before seeing a low cross cut-out.
But, despite a stoppage-time scramble in the Boro box, the Blues were unable to send the tie to a replay as their hopes of an FA Cup run were dashed.
Stevenage (4-4-1-1): Day; Smith, Jones, Ashton (c), Freeman; Andrade (Tansey 68), Heslop, Doughty, Akins; Morais (Deacon 84); Zoko (Burrow 90+2)
Goals: Zoko 8, 38
Subs not used: Arnold, Wedgbury, Parrett, Tounkara
Pompey (4-4-2): Carson; Moutaouakil (East 46), N’Gala, Bradley, Devera; Wallace, Ertl (c) (Holmes 72), Mahon, Barcham; Agyemang (Connolly 46), Bird
Goals: Connolly 70
Sent off: Mahon
Booked: Moutaouakil, Wallace
Subs not used: Smith, Painter, Cooper, Craddock
Referee: Gary Sutton
Attendance: 2,829 (1,005 Pompey fans)