Rell, 58, a Republican who ran on Rowland's ticket three times, took the oath of office shortly after noon on the north steps of the state Capitol.
"It has been a time of profound disappointment and disillusionment," Rell said in her inaugural address. "It has been a moment in history that we never thought we would see, and fervently hope that we never see again."
"Today, we begin to restore faith, integrity and honor to our government," she said. "It is our solemn obligation. It will be our lasting legacy."
Her address was repeatedly interrupted by applause from the hundreds who gathered on the Capitol lawn. Rell drew cheers when she said, "We must and we will recommit ourselves to ending the culture of corruption that has plagued our state for far too long."
Rowland, who has been under fire for accepting gifts from employees and state contractors, did not attend the inauguration; a spokesman had said he planned to spend the day with his family.
The announcement of Rowland's resignation came last week, just days after the state Supreme Court ruled that the legislative panel considering his impeachment could subpoena him to testify.
Rell, who became only the second woman to serve as governor in Connecticut, will serve out the remainder of Rowland's third term, which expires in January 2007.
Later Thursday afternoon, Senate President Pro Tem Kevin B. Sullivan, a Democrat, was to be sworn in as lieutenant governor.
The scandal-plagued Rowland had been on the sidelines since announcing last week he would resign. Rell had been the de facto governor, announcing members of her new administration, presiding over the State Bond Commission and discussing her plans for the remaining 2½ years of Rowland's term.
Brian Mattiello, Rowland's chief of staff who will serve as Rell's deputy chief of staff, said Rowland wanted it that way.
"I think he recognized the attention has turned to Lt. Gov. Rell and quite rightfully well," said Mattiello. "He wishes her well."
Even as Rowland left office, Rell announced she was issuing Executive Order No. 1, which imposes "strict ethics restraints on those who serve in government" and creates a new public integrity officer in her Cabinet.
On Wednesday, she said that some members of Rowland's staff who became known during the impeachment hearings will not be in her administration.
Rowland had come under fire for accepting gifts from state contractors, friends and politically appointed employees. He announced his resignation days before a House inquiry committee planned to recommend whether he should be impeached.
He continues to be a subject of a federal corruption investigation into alleged bid-rigging. Some of the same people who gave Rowland gifts, including improvements to his Litchfield cottage, are involved in the federal probe.
Rowland says he provided nothing in return to the gift-givers and did not compromise his office.
"I have great faith in Connecticut and its people, and I have great confidence in Lt. Gov. Rell's ability to lead this state," Rowland said in a short statement released Wednesday.