Blues star Havertz missed their 3-0 win over Rennes after testing positive for Covid-19 and is now in self-isolation.
But Werner scored twice from the spot and Tammy Abraham added a third against ten-man Rennes as Chelsea took a firm grip of Group E.
Blues boss Frank Lampard said: “I’ve spoken to Kai a couple of times. He’s very disappointed because he wanted to play.
“He’s isolating at home. He had mild symptoms. They escalated slightly today but he’s fine.
“Hopefully he comes back fine. We were all re-tested when we found that out and everybody else is negative.”
Werner, who took over penalty-taking duties from Jorginho, said: “Before the game the manager said when there is a penalty I should take it. Two today is crazy, not all days.
“I take it and good goals for a striker but hopefully I can go on like this. I am happy, I am happy Jorginho is cool with it.
“It is another point that speaks for our team, we are not selfish. We all go in one direction which is good. Now we want to win the group.”
Lampard said: “It was not an easy decision because Jorginho has been pretty faultless. He had missed two recently and Timo came in and scored.
“I had a word with Jorghino and his answer was perfect, he said he didn't mind who came in to take them he just wanted to score. Timo came in and scored so I am happy.”