The Pumas had started well and led 13-3 after 17 minutes, but Clerc's first try sparked a run of 21 unanswered points for France that saw the home side establish a 24-13 half-time advantage.
Argentina continued to battle hard in the second half and reduced the gap between the two sides to eight points on a couple of occasions, but they could not get any closer and Michalak's kicking ensured France would come out on top.
Meanwhile, Chris Ashton did not hold back in his criticism of England after they crashed to a 20-14 defeat by Australia.
Saturday's Twickenham result dealt a severe blow to England's hopes of being top seeds for the 2015 Rugby World Cup when the draw is made in London on December 3.
Ashton is thankful the tournament on home soil is still three years away because England need that time to sharpen their cutting edge.
England hung in as Australia dominated the first hour and Stuart Lancaster's men then bossed the final quarter - but they could not convert any of that pressure into points.
On four occasions, the first being with 22 minutes left in the match, captain Chris Robshaw opted not kick penalties at goal in search of a try that did not come.
"I think we cost ourselves the game. We had enough possession in their 22 and we just didn't take our chances," Ashton said.
Scotland captain Kelly Brown took encouragement from their belated but ultimately unsuccessful attacking fightback against South Africa, but has told his team-mates they cannot afford to wait so long against Tonga next weekend.
"The last 30 minutes it was either a case of lie down and die or stand up and fight, and I thought we stood up and fought," Brown said after the 21-10 defeat. "As a captain I want a side that is going to stand up and fight but next week we need to do that from the first whistle."