Having played their 3-0 midweek victory over Wycombe behind closed doors, the Blues fielded completely different line-ups in each half as the recently-appointed Portuguese boss gave all his players a chance to gain pre-season fitness at Fratton Park.
Villas-Boas' side failed to get out of second gear in the first period but took the lead in the seventh minute when Ben Haim calamitously headed into his own net.
Substitute goalkeeper Hilario produced a superb save to stop Luke Varney's penalty after the break to help Chelsea eke out victory on the south coast.
Villas-Boas chose to start the match with a blend of youth and experience, with the likes of Fernando Torres, Ashley Cole and Florent Malouda lining up alongside youngsters Billy Clifford and Tomas Kalas.
Portsmouth, meanwhile, made three changes to the side that beat Havant & Waterlooville on Monday as Herman Hreidarsson, Ben Haim and Stephen Henderson came in for Jason Pearce, Lewis Stockford and Jamie Ashdown.
Portsmouth came close to breaking the deadlock within the opening three minutes when David Norris burst down the left flank and only a smart block from Ashley Cole prevented the incoming Dave Kitson flicking home at the near post.
But despite the flash of attacking intent, it was the visitors that began the brightest and were given a lead through a bizarre own goal from Ben Haim.
Torres' cross from the right was mis-hit by Greg Halford as he attempted to clear, resulting in the former Chelsea defender heading into his own net.
Villas-Boas' troops continued to press after taking the lead, with Torres somehow heading a gilt-edged chance wide before John Obi Mikel fizzed a free-kick straight at goalkeeper Henderson.
Despite Chelsea's dominance, Portsmouth did muster a few chances of their own and tested Ross Turnbull on several occasions.
The former Middlesbrough keeper was first forced to stop Norris' bundled header sneaking home, before palming wide Luke Varney's thumping drive as half-time approached.
Chelsea started the second period with an entirely new XI, while Portsmouth - who could only name five substitutes - brought on Ashdown and Pearce.
The half began at a lackadaisical pace and the only moment of note was 30-yard free-kick from Hreidarsson.
However, the game soon livened up when substitute Hilario was adjudged to have brought down Luke Varney and referee Keith Stroud pointed to the spot.
The former Blackpool striker stepped up confidently but was thwarted by the Portuguese goalkeeper's outstretched hand down low to his left.
Dave Kitson flashed a shot wide as he looked to atone for Varney's miss, before Didier Drogba and Yossi Benayoun had efforts at the other end.
Hilario's good work twice almost came undone after defensive miscommunication saw Varney hare into the box to try and score, but Nathan Chalobah and Jose Bosingwa's blushes were spared by last-ditch defending on both occasions.