Han Sang-gyun, head of the Korean Confederation of Trade Unions (KCTU), surrendered to police on Thursday
He is accused of inciting violence at an anti-government rally on 14 November.
On Wednesday police began an operation to enter the temple to arrest him but delayed it on the request of the monks.
The monks warned said it would be an act of religious persecution for police to raid the temple.
"If the police raid the temple, it... will be tantamount to a state clampdown on the Jogye Order and on the whole Buddhist movement in South Korea," temple officials said in a statement.
Image captionThe police operation to seize him had already begun when the temple said Mr Han would surrender
As hundreds of police surrounded the temple on Wednesday evening, the executive chief of the temple held a press conference saying the Jogye Order would resolve the issue by noon on Thursday, after which police suspended the raid.
On Thursday, Mr Han finally emerged, paid his respects at the main temple, addressed his supporters and the media, and then gave himself up to waiting police.
South Korean religious venues, particularly Christian churches, were often used by political activists seeking refuge in the 1980s. There is no law preventing police from raiding such buildings but they have often opted not to.
Image captionThe rally was one of the biggest in the city in years
Those at the protest in November had a diverse range of grievances, from President Park Geun-hye's plans to make it easier to sack workers, to a decision to use only one, state-approved history textbook in the nation's schools.
The rally, which the government says was illegal, saw clashes between police using pepper spray and water cannon, and protesters, some of whom were armed with metal pipes and sharpened bamboo sticks.
The subsequent police crackdown prompted a smaller demonstration on Saturday - 14,000 people, rather than the 60,000 estimated at November's protest - to demand an apology from the president.
Ms Park has drawn the ire of labour unions and farmers for planning to make it easier to dismiss workers and to cap the salaries of senior employees. However, many of her labour market policies are more popular with the general public, according to polls.
The BBC's Stephen Evans in Seoul says there is an increasingly bitter division between South Korea's conservative government and its left-wing critics, who accuse it of diminishing democracy.
I simply had to say thanks once more. I'm not certain the things I would have made to happen in the absence of the actual solutions revealed by you over this concern. It was a very frustrating problem in my opinion, nevertheless understanding the very skilled style you managed it made me to weep with joy. I'm thankful for your guidance and even believe you know what an amazing job your are putting in training others using your site. I know that you've never met all of us. <a href="http://www.supremeoutlet.us.com" >supreme outlet</a> supreme outlet
I and also my friends appeared to be reading the excellent points on your web page while at once developed a terrible feeling I never thanked the blog owner for those tips. Most of the men came certainly excited to see all of them and already have pretty much been using those things. Many thanks for genuinely quite accommodating and for getting such tremendous guides most people are really desirous to discover. Our sincere regret for not expressing gratitude to you earlier. <a href="http://www.goyardhandbag.com" >goyard</a> goyard
I precisely wished to appreciate you again. I'm not certain the things that I could possibly have made to happen without the entire points shared by you regarding this problem. It actually was the hard scenario in my opinion, but taking a look at a expert technique you managed the issue forced me to cry for contentment. I will be thankful for this guidance as well as have high hopes you know what a powerful job your are providing training others through the use of your web site. More than likely you haven't come across any of us. <a href="http://www.kevindurantshoes.us.com" >kevin durant shoes</a> kevin durant shoes
Thank you for all your work on this web site. Gloria enjoys participating in investigation and it is simple to grasp why. All of us notice all of the dynamic medium you present powerful tactics on the web site and as well foster response from others on that situation plus our own girl is in fact studying a great deal. Take advantage of the remaining portion of the new year. You're the one performing a remarkable job. <a href="http://www.golden-goose.us" >golden goose</a> golden goose
I am just commenting to make you understand of the awesome encounter my daughter developed using your site. She mastered such a lot of things, which include what it's like to possess an incredible giving mindset to have the others with ease have an understanding of several tortuous things. You actually surpassed readers' desires. Many thanks for imparting the great, safe, revealing and also fun tips about your topic to Kate. <a href="http://www.yeezy350v2s.com" >yeezy 350 v2</a> yeezy 350 v2