During the persecutions suffered by Lithuanian Jewry in 1655 (a continuation of the massacres of 1648–49), R. Shabbetai was compelled to flee from Vilna to Lublin, but only three months later the rioters reached Lublin, and R. Shabbetai succeeded in escaping to Bohemia. He stayed first in Prague, and then for a time in Dresnitz, Moravia, after which he was appointed rabbi of Holesov, where he died. R. Shabbetai, who had a polished, elegant, and facile style of writing, also had a historical sense. He portrayed the Chmielnicki persecutions of 1648–49 in his Megillat Eifah (Amsterdam, 1651), in which he described the events and the sufferings through which the Jews of Poland passed during that era. This work is an important historical document and has been translated into German and Russian. He also composed selihot (publ. in Amsterdam, 1651), in which he poured out his bitter complaints. He charged his children and grandchildren always to observe the takkanot of the Councils of the Lands and to appoint the 20th of Sivan as a day of fast, on which they should recite the kinot he compiled.
His other works are: He-Arukh (Berlin, 1767), a commentary on the Arba'ah Turim, Yoreh De'ah of R. Jacob b. Asher; Tokfo Kohen (Frankfort on the Oder, 1677), on the laws of possession and undecided laws (teiku); Gevurat Anashim (Dessau, 1697), on chapter 154 of the Shulhan Arukh, Even ha-Ezer, to which are appended ten responsa written by his father; and Po'el Zedek (Jesenice, 1720), on the 613 commandments as enumerated by Maimonides, divided for the seven days of the week.
בשנת ת'ורי ז'הב נעשה ל'ך עם נקודות הכסף דף פ,ב-פב,א: קונטר' אחרון. השגות על "דף האחרון" לר' דוד ב"ר שמואל הלוי.