Argentina 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.
The Pumas 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.
Les Bleus stunned the Wallabies 33-6 in Paris last weekend but they have found Argentina a tough nut to crack and have only have triumphed in four of the 11 meetings between the two nations.
And another night of disappointment looked to be on the cards for the French at Stade Lille Metropole when, after Michalak had put them ahead with a penalty, Argentina promptly replied with a flurry of points.
A break from Gonzalo Tiesi helped centre Marcelo Bosch, who plays his club rugby in France for Biarritz, go over for the game's opening try in the fourth minute, and then Nicolas Sanchez added eight more points from a conversion and two penalties.
Argentina soon found themselves on the back foot though and a 17-minute 21-point scoring blitz from the French all but ended the South American nation's hopes of following up their win over Wales with another triumph.
Experienced winger Clerc collected two tries - taking his tally for his country to 34 - and flanker Yannick Nyanga crossed for another in quick succession as, with Michalak adding the extra points for each, the hosts powered into an 11-point lead at the interval.
There were no more tries in the second half, which turned into a shoot-out between Michalak and Sanchez.
Sanchez brought Argentina back within touching distance with two penalties and a drop goal, taking his personal tally for the evening to 17, but Michalak slammed the door shut with three more penalties in the final 12 minutes to seal France's triumph.
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