Freddie Read and Stan Bridgman were also on target for the young Blues at the club's Roko training base on Saturday.
Mark Kelly's troops took the lead after just seven minutes when Read's low free-kick from 20 yards outsmartedÂ the Grecian keeper.
And the hosts doubled their advantage in the 19thÂ minute through a magnificentÂ 25-yard strike from Maloney which found the top corner.
The Isle of Wight-born talent notched his second of the game nine minutes before half-time, although his drive took a fortuitous bobble over the diving keeper.
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However, the visitors came out with their tails up in the second period and scored just seconds after the restart.
A cross from the right was met by an Exeter striker, whose header beat Pompey keeper Leon Pitman.
The Grecians pushed for a secondÂ but the Blues were resolute, with Pitman making a few decent stops.
Maloney almostÂ grabbed a hat-trick on 59 minutes when he latched on to Josh Flint's long ball but the striker's shot was well saved.
But Kelly's men wrapped up the win with three minutes remaining.
Substitute Bridgman was alert to steal the ball off an Exeter defender before calmly slotting his right-footed shot home.Â
Pompey racked up back-to-back victoriesÂ and travel to Bournemouth next weekend.'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹'‹