Protesters shouted in the street as Lech Walesa attended the Catholic mass, in a reminder that many Poles are not ready to reconcile with Mr Jaruzelski, who oversaw violent crackdowns on pro-democracy activists before the Iron Curtain fell in 1989.
Mr Jaruzelski, who died on Sunday aged 90, declared martial law in 1981 to put down an uprising by Mr Walesa's movement, and his subordinates killed dozens of people.
Yet he has also been credited for his role in ushering in democracy in Poland.
Mr Walesa, 70, dressed in a black suit and black tie, sat at the front pew of the Cathedral of the Polish Army, alongside serving president Bronislaw Komorowski and former head of state Aleksander Kwasniewski.
About 300 protesters gathered outside the cathedral. Some shouted a traditional anti-Communist chant: "Hit the Red bastards with the hammer and the sickle!"