Kevin Nolan's stunning bicycle kick maintained Bolton's impressive start to the season and turned up the pressure on Portsmouth manager Alain Perrin.
Nolan provided an acrobatic finish from Kevin Davies' header after 24 minutes.
Pompey stepped up the pace after the interval, but Bolton survived to go third in the Premiership.
Nolan missed a chance to add a second, and Perrin's misery was complete when he was sent to the stand for an altercation with the fourth official.
The defeat left Perrin with only three wins from 15 games at Pompey, but he will be pleased with the application shown by his side, even though they left empty-handed.
Bolton boss Sam Allardyce restored Jay-Jay Okocha to his side, while Perrin recalled Laurent Robert in a bid to give Pompey a cutting edge.
Nolan and Davies had early opportunities as Bolton went straight on to the attack.
But they suffered a setback as they lost Gary Speed inside the first 10 minutes. He limped off to be replaced by youngster Joey O'Brien, making his first appearance of the season.
They recovered from the blow to take the lead in spectacular style after 25 minutes, courtesy of a wonder strike by Nolan.
Henrik Pedersen's cross was headed into the danger zone by Davies for Nolan to produce an overhead kick that left Jamie Ashdown helpless.
The impressive Hidetoshi Nakata almost produced another stunning goal eight minutes later, but his ambitious flick from Ricardo Gardner's cross was narrowly off target.
Pompey finally broke the shackles, with Brian Priske's driven cross just having too much pace for Dario Silva to connect.
Matt Taylor then tried his luck from 20 yards, but his shot flew straight at Jussi Jaaskelainen.
Priske produced another dangerous cross after 65 minutes, but once again no-one was on hand to apply the finishing touch.
Nolan squandered a glorious chance to make the game safe for Bolton when he ran clear seven minutes later, but screwed his shot wide from only 10 yards.
Pompey had shown plenty of purpose after the break, but the lack of a cutting edge was costing them dear.
Richard Hughes' long-range effort was on target, but Jaaskelainen was able to save comfortably.
And as the frustration grew, Pompey boss Perrin was sent off after he applauded the fourth official in ironic fashion.
Bolton manager Sam Allardyce:
"It was a great goal by Kevin Nolan, great technique and quality, and a vital win for us. We are on a magnificent run and we just hope we continue it.
"The fans here appreciate everything we do. The club has been on the up and up in recent years, but we are going beyond even my expectations.
"Portsmouth came to sit back initially, but once we scored they had to come out and it was an entertaining game. They might have got a goal with a better finisher, but we are pleased to have the points."
Portsmouth coach Joe Jordan:
"We're all very disappointed and very emotional. We had chances to get back in the game after the goal, but failed to take them.
"It's been a tough week, especially after the Carling Cup defeat to Gillingham in the week.
"There was encouragement in the first-half when we got the ball. When we got the chance we played well."
Bolton: Jaaskelainen, Hunt (Diouf 90), Ben Haim, N'Gotty, Pedersen, Speed (O'Brien 10), Okocha (Giannakopoulos 75), Nakata, Nolan, Gardner, Davies.
Subs Not Used: Walker, Borgetti.
Booked: Ben Haim, Giannakopoulos.
Goals: Nolan 25.
Portsmouth: Ashdown, Stefanovic, O'Brien, Priske, Vignal, Robert, Taylor (Karadas 66), Hughes, O'Neil (Songo'o 73), Silva (Todorov 85), Diao.
Subs Not Used: Westerveld, Skopelitis.
Booked: Stefanovic, Priske.
Att: 23,134
Ref: M Clattenburg (Co Durham).