His signature, capping nine years of legislative battles over the bill, came just hours after the Senate sent it to him Monday.
The law goes into effect July 1.
"It's a moderate, reasonable piece of legislation and I'm going to sign it," Pawlenty told reporters at an earlier news conference.
In addition to the waiting period, the new law requires that women asking for an abortion be given, among other things: estimates of the pain a fetus might feel; the probable gestational age of the unborn child at the time the abortion is to be performed; and the medical risks associated with abortions and with carrying a child to term.
Tim Stanley, executive director of the Minnesota chapter of the National Abortion and Reproductive Rights Action League, said it was "a sad day for the women of this state."
Eighteen states have adopted similar waiting-period measures.