Kathmandu, Feb 28: Mr Gomez, leader of the Knights Templar drug cartel, was arrested in Morelia in Michoacan state without a shot fired.
He was taken to Mexico City, where he was paraded before television cameras, before being flown by helicopter to a maximum security prison.
President Enrique Pena Nieto wrote on Twitter that the rule of law had been strengthened because of the arrest.
Police said they located him by following one of his messengers, part of a close network providing him with food and clothing.
He was captured when he stepped outside his house, wearing a hat and scarf to try to hide his identity.
Eight of his associates and several weapons, including a grenade launcher, were captured too. His brother, Flavio Gomez, who was in charge of the family’s finances, was also arrested.
Police spent months gathering intelligence for the operation and reportedly seized nearby properties in the weeks leading up Mr Gomez’s capture.
Analysis: Katy Watson, BBC News, Mexico City
For a man who reportedly said he would rather die than be captured, this must be a humiliating end. Paraded in front of millions of Mexicans on live television, he kept his head down as he was marched from a prison van to a police helicopter and flown to a high security prison.
While La Tuta’s capture may be a coup for the administration of Enrique Pena Nieto, the fallout in the state of Michoacan is not clear. It is a poor and violent part of the country, the battleground between drugs cartels and vigilantes trying to oust them.
As one security expert told me, this was a man who was not just in charge of a drugs empire – he wanted political power too and in politics you gain as many enemies as you do friends.
Perhaps that is what led to the net closing in in the end?
Previously a school teacher, Mr Gomez became one of Mexico’s most powerful drug lords and took control of Michoacan.
Known by his nicknames “La Tuta” and “El Profe”, referring to his former job, Mr Gomez ruled over much of Michoacan state as head of the Knights Templar cartel.
Mr Gomez evaded capture for years while other senior members of the gang and rival drug lords were captured or killed.
By the time of his arrest, he had a $2 million (£1.3 million) bounty on his head.
“With this arrest, the rule of law is strengthened in the country and [we] continue moving toward Mexico in Peace,” President Pena Nieto tweeted.
The arrest come as the president strives to assuage public anger over the abduction and apparent murder in September of 43 trainee teachers by police accused of being corrupt in concert with criminal gangs.
Knights Templar was primarily a drug cartel and it controlled a large part of the lucrative methamphetamine trade in western Mexico.
But it was also known for mixing in business and politics in the region and even took effective control over the state’s international port, Lazaro Cardenas, making millions of dollars from illegal mining of iron ore.
A federal government offensive in 2013 saw the Pena Nieto administration wrest back control of Michoacan state from the Knights Templar and rival gangs.
As leader of the biggest cartel in the region, Mr Gomez became the prime target of Mr Pena Nieto’s crackdown.
The administration has been criticised for failing to tackle the drug gangs, with vigilante groups forming to take on the dealers illegally.
Mr Gomez’s arrest comes just over a year after the capture of the country’s most notorious drug lord, Joaquin “Shorty” Guzman, head of the Sinaloa Cartel.
Unlike many rival gang leaders who carefully avoided the limelight, Mr Gomez regularly gave media interviews and railed against the government in Youtube videos.
Mr Gomez began life in the drug trade as an small-time marijuana dealer, before joining a Michoacan gang called La Familia and rising to a senior level. A split in La Familia led him to form Knights Templar.
A father of at least seven, Mr Gomez was also wanted by US authorities in connection with the 2009 murder of 12 Mexican federal police officers.