Emma Hayes branded Swedish referee Sara Persson's officiating "horrendous" after Lyon dumped Chelsea out of the Women's Champions League.
So-Yun Ji scored a fine free-kick but Chelsea could not topple European giants Lyon, who edged through to a fourth consecutive Champions League final at Kingsmeadow.
Eugenie Le Sommer's neat finish scrambled a 1-1 draw for a 3-2 aggregate victory for defending champions Lyon, who can add a fourth straight title to the 13th domestic league crown they sealed in midweek.
Hayes was left incensed by referee Persson denying Chelsea a penalty, hitting out at the general standard of officiating across Sunday's engaging clash at AFC Wimbledon.
"I'm going to take a fine for it, but I thought the referee was horrendous," said Chelsea coach Hayes. "You really want strong officials in big games.
"If hands are outside of what they consider a natural position it's a penalty but she didn't call it.
"She didn't manage the game, I think she was scared of them. She didn't control both teams."
Chelsea threw everything at Lyon in the second half, with captain Karen Carney curling a fine shot against a post and Drew Spence side-footing wide from just yards out.
Defeat means Chelsea cannot qualify for next term's Champions League as they are unable to finish inside the Women's Super League's top two.
Hayes felt Chelsea dominated Lyon and deserved to win, but lamented her side for lacking the vital killer instinct.
"This is probably the story of the team's season; I absolutely feel we've improved, but unfortunately we've been too much of a nearly team this year," said Hayes.
"We've gone toe-to-toe with the champions of Europe, we scared the life out of them and made them average.
"Lyon's seven-year dominance is massively threatened. It's the start of a new era in the women's game. We just would have liked to have progressed and put the nail in their coffin today.
"We deserve to be in the final but it's not about that, it's about goals. But I can't be critical, I'm so proud of my players."
Reynald Pedros accepted Hayes' assertion that the rest of Europe's big guns are catching up and threatening to end Lyon's dominance.
"Our rivals are getting stronger," said Lyon coach Pedros. "We're very much aware, we knew from our experiences once you get to the knockout stages, this year and last year, that other teams are getting stronger.
"But if we can stay strong against them that's great.
"We know we've got to work even harder than ever to stay ahead of the pack. We've just got to do everything we can to stay ahead."