The pipe ruptured near St. Mary's Street-143rd Street station about 4 a.m., an MTA spokesman said.
Regular service resumed about 10 a.m., according to the MTA's website.
The 6 train was suspended for six hours from Hunts Point Avenue to 125th Street, while 4 and 5 trains ran local.
Shuttle buses supplemented regular service though straphangers were still frustrated by the disruptions.
"It's frustrating. The train is much easier. It's much faster than a bus and it leaves me right in front of my job," said Angel Hernandez in East Harlem.
"It's inconvenient and annoying," said Yvette Soto, 36.
"These buses are slow and take too much time. They're also too crowded," Soto added. "It's not a good start to the week."