Abu Dhabi Ocean Racing's Azzam arrived at the Volvo Ocean Race safe haven Tuesday in fifth place, 15 hours behind the stage winner, Team Telefonica.
But skipper Ian Walker was not entirely disappointed at being the last boat to finish.
Stepping off the team's Volvo Open 70 yacht for the first time in 16 days, Walker said he had mixed feelings.
"I am upset not to have finished with a better result," he said.
"But, on the other hand, after the disaster of breaking our mast on Leg 1, I feel a strange feeling of relief to have at least completed the first part of the second leg.
"To have failed to make the stop-over in Abu Dhabi would have been absolutely disastrous for the team and the stopover."
The race from Cape Town to an undisclosed port in the Indian Ocean - kept secret because of concerns about a piracy attack - ended with Iker Martinez's Telefonica nosing out Camper/Emirates Team New Zealand by just one minute and 57 seconds after more than 50 days of sailing.
Puma Ocean Racing, who also suffered a broken mast in Leg 1, took third, with Groupama more than two hours behind in fourth.
After arrival, the boats were carefully loaded on a transport ship for safe passage to Sharjah, and from there they will make a one-day sprint to Abu Dhabi, arriving sometime early in the New Year.
Tuesday's finish was a discouraging result for the Abu Dhabi team after they held the lead in Leg 2 on five separate occasions. But they fell foul of a low-pressure trough that blocked the fleet's path for several days.
After making back more than 150 nautical miles on the leaders, a slow doldrums crossing all but sealed Azzam's fate.
"It has been a very bizarre leg, and one during which we have scarcely seen another boat after the first night despite a very conservative strategy," Walker said.
"Fifth place does nothing to help get us back up the leaderboard where we wish to be and every member of the crew is feeling the pain.
"One thing that gets to me is that the guys have sailed the boat pretty well and yet all the effort expended actually now counts for very little in terms of reward."
Walker said his crew would regroup at the safe haven and turn their focus to the sprint into their home port of Abu Dhabi.
"There is no shame in being beaten by any of the teams in this race, and the pain of finishing fifth will make the taste of future victories even sweeter," he said.
The mood was considerably brighter aboard Telefonica, which crossed the finish line with fist-pumps, screams, handshakes and hugs.
Martinez described the neck-and-neck finish with Camper as "the final miles of madness" with the pair switching the lead repeatedly until eight miles from the finish when Telefonica stole the lead.
Martinez said it was a very difficult game of "cat and mouse" that was played in the dark while dodging atolls.
"I've never navigated at night so close to the rocks and with so many complicated manoeuvres," he said. "A few miles from the finish we thought we had few chances to pass Camper, and there were three or four times during the night when we were left without wind.
"It was all a bit chaotic but luck changed sides, although the truth is either one of the teams could have crossed the line first."
Chris Nicholson, the Camper skipper, said his team learned a lot from the close-quarters combat with Telefonica.
"We had an amazing battle with Telefonica these last few days, and then we got rolled about an hour from the finish by one rogue cloud," he said. "Occasionally the sport can throw that up at you. Normally the good guys win. First of all Telefonica sailed a fantastic race, they really did, from start to finish. They were there to take the opportunities in the end."
Camper and Telefonica initially flagged protests against each other following the narrow finish, but after discussions the teams mutually agreed to drop them.
The five boats will now be loaded on to a ship - a risky manoeuvre that has never been done in the race before - and transported to a point off the Sharjah coastline, from where the leg will be completed with a day-long sprint to Abu Dhabi.
Team Sanya, the sixth boat in the fleet, was forced to suspend racing and head for Madagascar after picking up rigging damage while in the lead on Day 9. Their focus is on getting the boat in shape for Leg 3 into their home port of Sanya, China.