Yeddyurappa's former cabinet colleague Es En Krissnaiah Setty, who was co-accused, was present in the court when the orders were passed by Justice N K Sudhindra Rao. He was arrested and sent to judicial custoday.
BSY is accused of denotifying land in and around Bangalore for pecuniary benefits to his family and Setty.
Yeddyurappa's two sons -- Shimoga MP B Y Raghavendra and B Y Vijendra and his son-in-law R N Sohan Kumar were granted conditional bail after each furnished a surety bond of Rs five lakh. Yeddyurappa was not present in the court citing health reasons.
The court had issued the arrest warrant against Yeddyurappa asking the police to execute the same by Tuesday. The former CM stepped down from office on August 4 after the Lokayukta report indicted him in illegal mining.
Meanwhile, Yeddyurappa's house on Race Course Road, which was the hub of political activity even after he stepped down from office, had party leaders and workers gathering.
Bad day for party: BJP
The BJP said it was a "bad day" for the party as its former chief minister BS Yeddyurappa was sent to judicial custordy in graft cases but asserted senior party leader LK Advani's yatra would go through the state regardless.
This development would not affect Advani's anti-corruption yatra that is set to pass through the state on Oct 30 and Oct 31, state BJP chief KS Eshwarappa told reporters in this coastal town, about 350 km from Bangalore.
"This is a bad day for us," Eshwarappa admittde shortly after the Lokayukta special court in Bangalore rejected Yeddyurappa's bail plea and directed his arrest in two graft cases.
"The law will take its course and we are confident that Yeddyurappa will come out clean," he added.
He said Advani will not cancel the Karnataka part of his Jan Chetna Yatra against corruption. The yatra is scheduled to enter Karnataka from Kasargod in Kerala on Oct 30.
Advani is scheduled to address meetings in this town, neighbouring Udupi and at two other places, Honnavara and Ankola in Uttara Kannada district, on Oct 31 before crossing over into Goa.