Pompey are top of the bottom half of the table - and just three points off sixrh spot - after their second away League One victory of the season.
Matt Kennedy's low finish in the first minute of the second half, following up after Curtis Main's header came back off a post, was enough to give Kenny Jackett's team the spoils at Gillingham.
With Main and Kyle Bennett coming into the side in place of Brett Pitman and Drew Talbot, Oliver Hawkins was again Matt Clarke's central defensive partner.
Pompey were the better side and Kennedy, Bennett and Ben Close all gave the struggling Gills first-half scares.
The Kent side's best hope of a breakthrough came when Sean Clare went to ground in the area, but the referee was not interested in the hosts' penalty claims.
Jackett's team went 1-0 up within 30 seconds of the second half starting as Kennedy converted when Main directed a header from Nathan Thompson's cross against a post.
Gillingham had the ball in the net when Josh Parker headed in a cross from close range but his range was too close and an offside flag saved Pompey.
Bennett, Jamal Lowe and Clarke all went close to a killer second for Pompey late on but their failure to get it didn't matter as the Gills ran out of steam, to the displeasure of the home fans, who called for chairman Paul Scally to go.
Pompey boss Kenny Jackett told the club website: 'It keeps us in touch with the top teams and I don’t really think we’ve hit top form yet this season. We had good control of the game and saw a lot of the ball, while it was great to come away with the clean sheet.'
Pompey host MK Dons next Saturday.
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