Two goals from Stefan Maierhofer inside the opening half hour put Ian Holloway's men in control at the Riverside Stadium.
Although Emmanuel Ledesma pulled one back 10 minutes from time, the visitors held on to move up to 20th, one point clear of the relegation zone.
Millwall's victory completed a miserable day for Barnsley, who went down 1-0 at home to Leeds United thanks to Ross McCormack's 28th league goal of the season.
That result leaves Danny Wilson's side second from bottom and three points from safety.
Birmingham City are just a point above the relegation zone after Matt Derbyshire's second-minute strike saw them fall to a 1-0 defeat at Nottingham Forest.
Goals from Albert Riera, Gabriele Angella and Lewis McGugan sealed the win for Watford, and there are five points between Brighton and Hove Albion in sixth and Giuseppe Sannino's men in 12th.
Danny Hollands restored Portsmouth's lead shortly before the break and, although Harrold levelled again almost immediately, Wes Fogden's winner worsened Rovers' plight.
Gary Rowett's men lie fifth, four points behind Rochdale in third, while Hartlepool remain 19th, just two points above the bottom two.
