A diving header from Michael Brown helped Portsmouth survive a potential banana skin and book their place in the second round of the Carling Cup.
Nadir Ciftci's gave the south coast side a dream start, his close-range header from a Pompey corner opening the scoring on eight minutes.
Stevenage, in their first ever League Cup tie, grabbed an equaliser ten minutes later as Darren Murphy's 20-yard drive was deflected past the helpless Jamie Ashdown.
But Brown's goal nine minutes before half-time proved sufficient for last season's FA Cup finalists to take the victory.