The 28-year-old will travel with the team but is expected to make his return to action in the game against Leinster in the Heineken Cup a week on Sunday.
Ben Cairns will replace Paterson at the Stade Armandie, while Craig Smith comes in for for Alasdair Dickinson in the front row and Ross Rennie starts in place of Alan MacDonald at flanker.
Howells said: "We have given Chris Paterson as much time to recover from his knee injury as possible and he will travel with the team to France.
"You have to approach European games in a different way as a round-robin competition poses different problems to a league campaign.
"Agen are more physical than some of the opposition we face most weeks and their back-line displays great French flair.
"Last week we played great rugby with some great phases, and when we didn't have the ball, we defended well.
"It wasn't that Munster played badly, we stopped them playing well."