While Mourinho said he was right to leave Radamel Falcao and Loic Remy at home after Chelsea lost their Group G tie against his former club, Wenger defended replacing goalkeeper Petr Cech with David Ospina after his team fell to their second defeat in Group F.
Mourinho, whose Chelsea side are struggling at 14th in the Premier League, indicated before the game he would ring the changes, and duly left Remy, Falcao and Oscar at home, while Eden Hazard was restricted to the bench.
The decision to travel without an extra striker backfired, as the Portuguese did not have an established forward to call upon despite seeing his team fall behind twice in the 2-1 defeat.
When asked if he regretted leaving Falcao and Remy behind and whether they were being punished for their poor form, Mourinho said: "No."
"No punishment, no punishment. Just a decision," he added.
Chelsea are now third in Group G behind Porto and Dynamo Kiev. Mourinho said his team did not play poorly.
"It's normal, when the team are not winning matches, you have to make changes, but games like today are difficult to analyse because the result doesn't mean you played badly," he said.
Wenger was in a far more irritable mood after the 3-2 defeat by the Greeks resulted in his choice of keeper being questioned.
The game hinged on a calamitous mistake by Ospina, who failed to collect an inswinging corner and let the ball drop over the line, gifting Olympiakos a 2-1 lead five minutes before the break.
"You cannot select the team by making a poll before the game and getting everyone's opinion," Wenger said. "It's always a simple thing to say Ospina shouldn't have played.
"No goalkeeper is mistake-free -- it could have happened to Petr Cech as well.
"But I don't have to sit here and give you an explanation of every decision I make. We did not lose the game because of that mistake, that's a farce."
(Reporting by Simon Jennings in Bengaluru; editing by Sudipto Ganguly)
