Searing heat, high humidity and a bumpy Marina Bay Street Circuit under 1500 halogen lights always make for a difficult combination, and so it proved, but the defending champion was fastest at the end of both 90-minute runs, especially on the significantly quicker supersoft tyre being used for the first time since Canada.
Vettel, 39 points behind the championship leader, Fernando Alonso, was satisfied enough with his lap of one minute 48.340secs, which was more than two seconds faster than his time in FP1 on the soft rubber.
"This is a tough circuit for drivers and cars, but overall we can be happy with today," the German said. "Today's results are not so conclusive as some drivers got stuck in traffic, but most important is that the car seemed to work on either tyre."
Ferrari tried out a raft of new components on their car as they seek to help Alonso win his third world title, and he was third quickest, just over half a second down.
The Spaniard said: "Overall, I would say today was positive even if the first impression is we are not as competitive as we were in Monza two weeks ago.
"But we still lack some performance on tracks like this one where you need maximum aerodynamic downforce."
McLaren's Lewis Hamilton, second to Vettel early on, had to settle for fifth in FP2. His team-mate Jenson Button was second quickest, 0.311secs adrift, but complained of balance issues.
Hamilton said: "I was comfortable with the car, the guys have done a great job. It feels a lot different to the last race where there is a lot less downforce, so it's great to be able to throw the car around a little more without it sliding."
Hamilton, who has won two of the last three races to move within 37 points of Alonso, added: "Although the race pace felt pretty poor for me, I heard it was worse for others, which is comforting.
"We're obviously in the top five, but it's very close and qualifying is going to be tough. We just need to keep working on the route we're on."
Paul di Resta pipped his Force India team-mate Nico Hulkenberg to finish sixth-fastest. Kimi Raikkonen, a point behind Hamilton in the standings, was far from content with his Lotus after finishing 12th and two seconds back.
"We don't have enough grip for some reason, the Finn said. "I think we can improve tomorrow, but we have to find two seconds to the front.'