O'Mara argued that Zimmerman should not be jailed because the state's case is weak and his claim of self-defense is strong.
The original bail of $150,000 was revoked last month after Lester learned Zimmerman and his wife, Shellie, had failed to disclose more than $150,000 in donations from the public.
The judge's order Thursday said that the new $1 million bond was not a punishment but an amount that assured the court that Zimmerman would not abscond.
Zimmerman has the money to pay for his release, the court said.
In his ruling, Lester wrote about the first bond hearing and noted an undisclosed second passport kept in Zimmerman's safe deposit box.
"Notably, together with the passport, the money only had to be hidden for a short time for him to leave the country if the defendant made a quick decision to flee," the judge said. "It is entirely reasonable for this court to find that, but for the requirement that he be placed on electronic monitoring, the defendant and his wife would have fled the United States with at least $130,000 of other people's money."
Lester wrote the defendant's plans to flee were "thwarted."
Zimmerman, 28, is charged with second-degree murder in Martin's February 26 shooting death. Under Florida law, second-degree murder is a bondable offense.
Prosecutors had asked for bond to be denied or, if not, for it to be set at $1 million.
Martin family attorney Benjamin Crump said the parents preferred that Zimmerman remain in jail, but "they respect the ruling of the court and the strong message that the judge sent that deference to judicial integrity is paramount to all court proceedings."