Ousmane Dembele's second-half strike settled matters at the Jose Zorrilla against last season's LaLiga123 play-off winners.
Valladolid thought they had equalised through Keko in second-half stoppage time, but the goal was ruled out for offside after a VAR referral.
It was a far from convincing display from Ernesto Valverde's side, but it means they move top of the table ahead of Sunday's fixtures, while Valladolid are still looking for their first goal and win of the season.
Barca recalled Philippe Coutinho to the starting line-up but struggled for rhythm in the first half, with Dembele wasting the best of the early chances following a fine cushioned pass from Lionel Messi.
Dembele remained the most threatening of the champions' attackers, though, and made the most of his next good chance, sending a controlled volley past former Barca goalkeeper Jordi Masip 57 minutes in after a header down from Sergi Roberto.
Valladolid responded well to the setback and looked the most likely to score next, with Marc-Andre ter Stegen saving from Keko and Kiko Olivas in the final 15 minutes.
Luis Suarez had what he thought was the decisive second goal disallowed for offside, but Barca held on to make it two wins and no goals conceded from two league games this term, although it took a VAR intervention to deny Keko's last-gasp header.
What it means: Barca top but well short of their best
It never really looked like Barca would lose this game, but they certainly made hard work of trying to win it.
The champions struggled in the first half against Deportivo Alaves last week, so it was no surprise to see Coutinho brought back into the starting line-up, but they fared little better for most of the first hour here.
Still, they are nothing if not patient under Valverde, and Dembele took his goal very well given his earlier misses. Once they had the lead, they rarely looked likely to surrender it.
It means they are top of the standings with a maximum six points, but they have yet to produce a performance this season to make the rest of Spain – or Europe – unduly worried.
Pat on the back: Roberto stakes claim for regular spot
Back at right-back for this game, Roberto gave himself a real chance of supplanting Nelson Semedo as first-choice pick.
He had plenty of defending to do as Valladolid concentrated their attacks down their left, but he rarely put a foot wrong, while he also bagged the assist for the winner.
Boot up the backside: Messi goes missing
Messi effectively dragged Barca to three points last week, but he more or less forced them to get their latest win without him.
He had just one touch in the Valladolid box in the first half, wasted two promising free-kicks and was lucky not to be booked for a deliberate handball. It certainly was not his day.