Reeco Hackett's first goal of the season was not enough for City in their first home match of the Championship season.
Ryan Kavuma-McQueen and Adrian Segacic made it hard for the Imps after scoring in the first 14 minutes of the game.
City looke to pull the game back with a penalty, scored by Reeco Hackett, but Pompey got the final goal by Ebrima Adams which ended the game.
The Imps had their first attempt on goal in the first minute with a free kick, just outside the box. This was followed by three consecutive corners, all placed onto heads in the goal area but they were cleared by the Pompey defenders.
City got another chance after four minutes when Dom Jefferies went one on one against away goalkeeper, Nicolas Schmid, who got a hand to the ball after Jefferies' attempt.
Pompey scored after seven minutes when Kavuma-McQueen ran to get the ball outside the box and shot it into the bottom right corner of the goal.
George Wickens made a great save after 12 minutes from a shot that was chipped up to the top left of goal, but the goalkeeper caught the ball and got rid of any further danger.
The visitors made it two when they were awarded a free kick on the edge of the box after 14 minutes and Segečić blasted it into the back of the net with an unstoppable.
The Imps got an opportunity after 22 minutes when Hackett crossed a corner to the back post where many heads were, but it eventually rolled out of play for a goal kick.
Hackett got a goal back for City after the Imps got a penalty following from a Pompey player handballing in the box. Hackett powered the ball down the centre, while Schmid dove to the left after 32 minutes.
Goalscorer Hackett had another chance after 37 minutes when he got the ball in an area by himself and made a blind shot, but it went wide.
Wickens made another important save after 44 minutes following a chipped shot by Colby Bishop.
The second half began with mainly back and forth across the pitch before City made a change after, seeing Tendayi Darikwa come off for Andre Coubis after 54 minutes.
Pompey responded with a double change after 57 minutes where Kavuma-McQueen and Rocco Shein were replaced by Joshua Murphy and Adams.
The Imps got an opportunity after 64 minutes when Hackett took a corner landing at the back post before being cleared shortly to Hackett again who was able to get a shot toward goal but Schmid caught the ball.
City made a double change after 66 minutes of Varfolomeev and Jefferies for Tom Bayliss and Rob Street.
Pompey scored after 69 minutes when substitute Adams struck the ball outside the box and it fired into the back of the net, unable to be saved.
The Imps made another double change after 75 minutes with Draper and House replaced by Olaofe and Melia. Pompey were forced to make a change of Murphy to Marko Milanovic Marezi after 77 minutes.
City had a chance after 85 minutes when a cross into the Pompey box caused Olaofe and a defender to go toe-to-toe, but it went out narrowly wide.
Pompey made another double change of Marlon Pack and Abu Kamara for Joshua Knight and Brooke-Smith after 89 minutes.
The Imps had their final opportunity of the game after 93 minutes when Street chipped the ball toward the area, but a goal-line clearance led to it going out of play.
Imps: Wickens, Darikwa (Coubis 54’), Reach, Hackett, McGrandles, Jefferies (Street 66’), House (Melia 75’), Hamer, Varfolomeev (Bayliss 66’), Elerewe, Draper (Olaofe 75’).
Subs not used: Gauci, Towler, Elder, Konak.
Pompey: Schmid, Arthur, Shaughnessy, Pack (Knight 89’), Bishop, Segečić, Kamara (Brooke-Smith 89’), Shein (Adams 57’), Swanson, Devlin, Kavuma-McQueen (Murphy 57’) (Marezi 76’).
Subs not used: Bielicai, Swift, Bailey, Dia.
Attendance: 10,545