The verdict found Ghailani, accused of participating in the 1998 bombings of U.S. embassies in Africa, guilty of conspiracy to damage or destroy U.S. property with explosives, a charge that can carry a penalty of 20 years to life.
"We respect the jury's verdict and are pleased that Ahmed Ghailani now faces a minimum of 20 years in prison and a potential life sentence for his role in the embassy bombings," Matthew Miller, a Department of Justice spokesman, said in a written statement.
"He will face, and we will seek, the maximum sentence of life without parole when he is sentenced in January," added Preet Bharara, the U.S. attorney for the Southern District of New York.
The case, while a narrow win on the merits for federal prosecutors, can be seen as a setback for the Obama administration's goal of trying Guantanamo detainees in civilian courts rather than before military tribunals.
In this case, a 2001 superseding indictment charged Ghailani of conspiring with Osama bin Laden and other members of al Qaeda to kill Americans anywhere in the world, as well as separate charges of murder for the deaths of each of the 224 people killed in the U.S. embassy bombings in Tanzania and Kenya and various other offenses related to the bombings.
While the Department of Justice emphasized that Ghailani will get a lengthy jail sentence, critics are likely to play up the notion that a military court would have been a tidier way of dealing with the case and issues such as torture and treatment detainees may have experienced.
Already, a leading critic of the Obama administration's plan for civilian trials, Rep. Peter King, R-N.Y., the ranking Republican on the House Committee on Homeland Security, said he is "disgusted at the total miscarriage of justice today in Manhattan's federal civilian court."
"This tragic verdict demonstrates the absolute insanity of the Obama administration's decision to try al Qaeda terrorists in civilian courts," King said in a written statement.
In Ghailani's case, a key government witness was not allowed to testify in part because of allegations of torture and how they might have impacted the witness testimony.
"This case was doomed from the beginning when the judge excluded DOJ's key witness who admitted selling the explosives to Ghailani," King said. "Where is the justice for the more than 200 people killed and 4,000 injured in the terrorist bombings of our U.S. embassies in Kenya and Tanzania?"
Nonetheless, a proponent of civilian trials, a professor who has defended a Guantanamo Bay client, remained convinced civilian trials are the correct way to go.
"I agree that it's a setback for the administration, but in a way that reinforces, rather than undermines, the case for civilian court prosecutions," said Stephen I. Vladeck, a law professor at American University Washington College of Law in Washington, D.C. "The risk of acquittal is exactly why civilian trials are more legitimate than military commissions, and today's result bears that out."
Ahmed Khalfan Ghailani's Time Held by CIA Complicated His Prosecution
Ghailani, an accused al Qaeda operative, was facing 286 separate counts for his alleged role in the deadly bombings of the U.S. embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya on Aug. 7, 1998.
The Tanzanian national was held at the detention facility at Guantanamo Bay, Cuba, from September 2006 until he was transferred to New York in June 2009 to face trial in a civilian court.
Ghailani originally was indicted in 1998. The superseding indictment, for which he is facing trial, was returned in March 2001.
Captured in July 2004 in Pakistan, Ghailani was part of the CIA's High Value Terrorist Detainee Program before being transferred to Guantanamo Bay.
Ghailani's prosecution showed the complexity of trying former CIA terrorism detainees in civilian courts.
U.S. District Court Judge Lewis Kaplan denied prosecutors from allowing their key witness, Hussein Abebe, to testify. Kaplan ruled that the information that led to Abebe's arrest in August 2006 was obtained from Ghailani while he was in the CIA's program and exposed to enhanced interrogation techniques.
"There's no question," said Jim Cohen of Fordham Law School, "[that] they [prosecutors] were hamstrung" by Kaplan's ruling.
"One of the things we should read into it is juries are not necessarily going to be so appalled by the crime itself that they will give unfair consideration to the defendant," Cohen added. "It shows a detainee charged with these sorts of crimes can get a fair trial in the civil system."
The verdict came two days after a note from one of the jurors indicated that she wanted to be removed from the deliberations and noting that she felt she was being "attacked" by other jurors.
ABC News' Ariane de Vogue, Michael S. James and Shimon Prokupecz contributed to this report.