A Gabriel Tamas own goal put the hosts ahead four minutes before half-time and Junior Hoilett doubled the lead less than two minutes after the break, but it was an incident in the 68th minute that really riled the Baggies boss.
After Rovers debutant Jermaine Jones felled Peter Odemwingie with an ill-advised lunge, Clattenburg was quick to blow his whistle but, to Albion’s disbelief, gave only a free-kick on the edge of the area when the offence looked to be at least a yard inside.
Di Matteo felt it was the latest in a string of decisions to go against his team, saying: “I think, apart from the referee, everybody else thought we should have had a penalty.
“It’s not the first time. I’m fed up with talking about this after games because it’s happening almost on a weekly basis against us. It’s incredible.
“It’s a foul and it’s a penalty and I don’t know how he saw it outside the box. It was clearly inside, it wasn’t even on the line.”
But, while that decision was clearly a moment of misfortune for West Brom, they were also architects of their own downfall, particularly with the goal that put Blackburn ahead.
A well-contested first half had featured chances at both ends but none clear-cut until Tamas powered a header into the top corner under only slight pressure from Roque Santa Cruz.
The Romanian was sent off when the sides met at The Hawthorns three weeks ago and another afternoon to forget was complete just after the break as Hoilett easily beat the defender before lashing in Rovers’ second.
Tamas could certainly have done better but the 20-year-old Canadian still had plenty to do before he could celebrate his first Premier League goal.
Jerome Thomas stood out for the Baggies with an impressive display of wing play but Rovers keeper Paul Robinson was on top form, with one fingertip save to keep out Thomas’ curling effort.
For Blackburn boss Steve Kean, the result - Rovers’ third home win in succession - was the perfect way to celebrate the new long-term contract he signed this week. The win lifted Rovers up to seventh.