West Brom looked set to inflict a first Premier League defeat on Jose Mourinho at Stamford Bridge after goals from Shane Long and Stephane Sessegnon had overturned Samuel Eto'o's opener for the Blues.
However, referee Andre Marriner awarded the home side a spot-kick in stoppage-time when he ruled that Steven Reid had brought down Ramires.
Clarke felt it was a poor decision and was left to bemoan another couple of dropped points in a frustrating season so far for the Baggies.
He told Sky Sports: "My take on it is that it is no penalty. That is five points my team have lost this year because of late decisions on penalties.
"Southampton got a soft one, we had a stonewall penalty against Stoke which we didn't get, and the decision today which cost us another two points.
"I'm sad, I'm angry, but I am also very proud of the players because we were magnificent today and deserved to get the three points.
"It is disappointing to take but if we carry that form into the rest of the season we'll be good."
Clarke was pleased with the way West Brom carried out the plan that he had set out, containing Chelsea for long periods and carving out opportunities as the game wore on.
He explained: "We defended well, we kept a good shape and frustrated Chelsea, which is what we set out to do.
"We responded really well in the second half and created a number of chances. We had a great chance to make it 3-1 before the non-penalty."
Clarke added: "Instead of being up close to the top six we are stuck in mid-table, and sometimes because it is little West Bromwich Albion.
"We want fair decisions when we come to these stadiums and I don't think today we got the decisions in our favour."