"You will now decide where the truth lies," U.S. District Judge Miriam Goldman Cedarbaum said.
The judge spoke for more than 90 minutes, spelling out the legal requirements the jury must find to convict Stewart or broker Peter Bacanovic on any count.
"You are to discharge this final duty with complete fairness and impartiality," she said. "You must have no bias or prejudice for or against the government or the defendants."
CBSNews.com Legal Analyst Andrew Cohen reports the judge made it clear that the jurors cannot infer anything from the fact that neither Stewart nor Bacanovic testified.
Cedarbaum dismissed the six alternate jurors who have sat for the full trial, but instructed them not to discuss the case with anyone because they could be called back if a juror cannot serve.
The judge instructed the jurors that they can find one of the defendants guilty but not the other, reports CBS News Correspondent Cami McCormick.
Within minutes of beginning their deliberations, the jurors sent the judge a note asking whether they could eat lunch with the excused alternates.
The judge, citing a "bond" the jurors developed during the trial, allowed the joint lunch but said she would tell jurors to suspend their deliberations while in the presence of the alternates.
Stewart is accused of conspiracy, obstruction of a Securities and Exchange Commission proceeding and two counts of lying to investigators. She could face up to 20 years in prison if convicted, although she could serve as little as one year. Bacanovic was charged as a co-conspirator.
Stewart faces four federal counts and Bacanovic five related to the sale of about $225,000 worth of ImClone stock on Dec. 27, 2001, the day before the stock plummeted on news that the government declined to review the firm's cancer drug.
Cohen said it may be some time before the jury returns with its verdicts.
"This jury has an awful lot of work to do," he said. "There are eight counts, nine charges, against both of the defendants, a lot of details and facts that they have to resolve, so I do not expect them back any time soon."
Attorneys on either side of the Martha Stewart stock case got their final chance to sway jurors Tuesday, with prosecutors saying "smart people do dumb things" and defense attorneys saying her acquittal would be "a good thing."
Cohen gave high marks to Stewart attorney Robert Morvillo.
"Robert Morvillo presented as fine a summation as I've seen in years. He reportedly charges $650 an hour, and for my money he is worth every penny Stewart has paid him to defend," said Cohen.
During closing arguments Tuesday, Morvillo insisted his client had a standing agreement with her broker to sell her ImClone Systems stock and was telling the truth when she later told investigators she did not recall being tipped off that ImClone's founder was trying to dump his holdings.
"Martha Stewart's life is in your hands," Morvillo told the federal jury. "I ask you to let her return to her life, and improving the quality of life for all of us. If you do that," he added, echoing the homemaking expert's slogan, "it's a good thing."
In a brief rebuttal, prosecutor Karen Patton Seymour challenged Morvillo's suggestion that the alleged conspiracy was too stupid to be true.
"Smart people make mistakes, and smart people do dumb things," she said. "Your common sense tells you that that's what white-collar criminals do every day."
The judge dismissed a securities fraud count against the domestic diva last week. The charge accused her of deceiving investors in her own media company by claiming she sold the ImClone stock because it reached $60.
The remaining counts against Stewart — conspiracy, obstruction of an SEC proceeding, and two counts of lying to investigators — carry up to 20 years in prison, but the federal sentencing guidelines would greatly reduce the term for both to about a one-year sentence per charge per person, says Cohen.
Bacanovic faces 25 years if convicted, but could have his sentence similarly reduced if convicted.