Comfortable 4-0 victors in the reverse encounter, Ernesto Valverde's men enjoyed no such dominance in Eindhoven as they came under heavy scrutiny for long periods.
The visitors had the woodwork to thank for denying PSV a lead on three occasions, before captain Messi took charge in the second half.
He broke the deadlock with a sublime piece of penalty area composure and then delivered the set-piece from which Gerard Pique ensured a late Luke de Jong header would be nothing more than a consolation.
PSV's bright start could well have come with early reward through Gaston Pereiro.
The winger forced Marc-Andre ter Stegen into a flying save from a free-kick, stroked a shot on to the right post and then, from De Jong's knock-down, spooned over from close range.
Arturo Vidal was twice denied by goal-line blocks before Barca survived another fright, Denzel Dumfries hitting the upright following De Jong's header against the crossbar.
3 - PSV are the first team to hit the woodwork three times in a Champions League game v Barcelona since Atlético de Madrid in April 2014 (also 3). Denied.— OptaJohan (@OptaJohan) November 28, 2018
Ter Stegen remained under scrutiny after the interval and yet, in the 61st minute, Barca were ahead.
Ousmane Dembele slipped a pass into Messi's path and the star man did the rest, weaving around multiple markers before rifling past an unsuspecting Jeroen Zoet.
And it was the skipper who also created what proved the winner 20 minutes from time as he deceived PSV's wall by whipping a free-kick onto Pique's boot for an instinctive first-time finish.
There was time left for Netherlands striker De Jong to nod home Angelino's cross in the 82nd minute, but Barca held on to three points despite squandering a clean sheet.
What does it mean? Messi's magic suitable for all occasions
Barca needed a spark and, as he so often does, Messi provided it. That the Argentine's wizardry was enough to make up for a sluggish team performance serves as an ominous warning to fellow Champions League contenders.
10 - Lionel Messi has netted 10 goals against Dutch opponents in five Champions League games (6 v Ajax, 4 v PSV). Habit.— OptaJohan (@OptaJohan) November 28, 2018
Dembele a handful
France international Dembele carried the confidence gained from his weekend goal into a promising performance at Philips Stadion, regularly threatening on the counter and teeing up Messi to open the scoring.
Shaky Rakitic emblematic of Barca battles
Fortunate that a loose pass out of defence went unpunished in the first half, Ivan Rakitic summed up Barca's anxiety. He was often panicky in possession and wasted a good chance to double the advantage after Messi's opener.
Key Opta facts:
- Lionel Messi has scored 15+ goals for Barcelona in each of the last 13 seasons in all competitions.
- Barcelona’s Gerard Piqué is the defender with the third-most goals scored in Champions League history (13) – only Iván Helguera (15) and Roberto Carlos (16) have more than him.
- Barcelona goalkeeper Marc-André ter Stegen made eight saves against PSV, more than in any other game this season in all competitions.
- Barcelona faced 23 shots against PSV, more than they’ve faced in any other game this season in all competitions.
- PSV are the first team to hit the woodwork three times in a competitive game v Barcelona since Atletico Madrid in April 2014 (also three), both in the Champions League.
- Ousmane Dembele has been involved in five goals in his last six games for Barcelona in all competitions (two goals and three assists).
- PSV are winless in their last 13 Champions League games (D5 L8), the longest such run of any Dutch side in the competition.
- Barcelona have lost just one of their last 27 Champions League group stage games (1-3 vs Man City in November 2016), and are unbeaten in their last 12 (W10 D3).
The LaLiga champions host Villarreal on Sunday as PSV visit Feyenoord. Both clubs wrap up their Champions League group stage commitments in December, Barca entertaining Tottenham and the Dutch side venturing to Inter.