Marriner pointed to the spot deep into injury time as West Brom led on Saturday after Steven Reid was adjudged to have brought down Ramires inside the area.
Eden Hazard converted to earn a point for the home side and ruin West Brom's hopes of a first league win at Stamford Bridge since 1978.
Samuel Eto'o had put Chelsea ahead in the last minute of the first half, but goals from Shane Long and Stephane Sessegnon put West Brom in charge.
West Brom looked set to claim all three points until the late controversy left former Chelsea player and assistant manager Clarke livid with the manner in which the game changed.
"It's ridiculous to have to take it because it isn’t a penalty," the Scot said after the match.
"That's five points my team have lost because of late decisions on penalties. Instead of being up close to the top six, we are in mid-table.
"I'm sad and I'm angry but I'm also very proud because we were magnificent. We deserved the three points and I'm proud of my players."
Clarke – who worked as assistant under opposite number Jose Mourinho – was happy with the way his team went about the game.
He added: "We were good, we didn't pass the ball well enough in the first half.
"We defended well, kept a good shape and frustrated Chelsea which is what we set out to do.
"We were disappointed to lose a goal just before half-time, but we responded really well, created a number of chances and had a great chance to make it 3-1 before the non-penalty.
"If we carry that form into the rest of the season we'll be good."
