The Finn's progress contrasted with that of McLaren's interim Honda-powered car, its eagerly-anticipated first official runs not coming until the afternoon due to early electrical issues.
When it did appear, the team's official reserve driver and GP2 runner-up Stoffel Vandoorne stopped out on track on only his second lap. The Belgian was able to get out for one final tour in the closing minutes of the session, ending the day with three laps under his belt.
"We'd hoped to get a few more laps today, but we had a fuel data-logging issue that stopped the car a couple of times," Vandoorne explained. "However, the team are already analysing the situation and we'll hopefully cure it ahead of tomorrow. Nevertheless, it's been a very positive day for us. At this stage of development, any lap we complete has a benefit – and it's better to be solving these initial teething problems in November rather than in Jerez next February."
Kimi Raikkonen helped Ferrari finish second overall, while his 2015 team mate and four-time world champion Sebastian Vettel spent time in the team's garage meeting his future crew members.
Nico Rosberg was half a second down on Raikkonen in the all-conquering Mercedes F1 W05 Hybrid, which he was driving just two days after the agony of his title defeat. The German completed 114 laps - more than any other driver.
Recently-crowned GP2 champion Jolyon Palmer was fourth fastest after an interrupted day with Force India. An engine issue restricted his morning running, while further technical gremlins meant more time was lost in the afternoon, his car rolling to a halt on circuit and triggering one of several red flags.
The Briton did at least manage to get going in the final hour and jumped into third, only to be demoted when Rosberg edged him by just 0.004s late on.
"I really enjoyed my first experience at the wheel of a Formula One car," Palmer said. "Despite a few technical issues early on, in the end we managed to get back on track and have a solid hour of running, getting up to speed fairly quickly. Sahara Force India is a team that gives young drivers good chances and I would love to get a role with them."
Carlos Sainz Junior, this year's Formula Renault 3.5 champion, was fifth fastest in the Red Bull RB10, fractionally ahead of Will Stevens, driving for Caterham after making his Grand Prix debut with the team on Sunday. Both Sainz and Stevens broke into triple figures in the lap count.
Lotus reserve driver Charles Pic was seventh, with Marcus Ericsson - testing for Sauber, with whom he will race next season - and Toro Rosso's 2015 rookie Max Verstappen rounding out the top nine ahead of Vandoorne.
Verstappen also had an interrupted day as a suspension issue put him into the barriers on only his third lap, though he was able to return to the track in the final hours of the afternoon.
"Unfortunately we didn't get much running in the morning, but in the afternoon we carried out very useful long runs, which helped me with my understanding of how to manage the tyres," he reflected. "To be able to run the car for a longer period than just an hour and a half, which is all I had done so far when running in the FP1 sessions, was definitely a good experience and lap by lap, I got more used to the car."
The Dutchman will stay in the STR9 for the second and final day of the Abu Dhabi test. Stevens at Caterham and Vandoorne at McLaren will do likewise, but the rest of today's field will switch.
Among the new faces will be Ferrari protege and GP2 racewinner Raffaele Marciello, Mercedes reserve driver Pascal Wehrlein, and Alex Lynn, this year's GP3 champion and a member of Red Bull's junior team, who will test for Lotus.
Unofficial Tuesday times from Abu Dhabi:
1. Valtteri Bottas, Williams, 1m 43.396s, 80 laps
2. Kimi Raikkonen, Ferrari, 1m 43.888s, 81 laps
3. Nico Rosberg, Mercedes, 1m 44.512s, 114 laps
4. Jolyon Palmer, Force India, 1m 45.516s, 37 laps
5. Carlos Sainz, Red Bull, 1m 45.339s, 100 laps
6. Will Stevens, Caterham, 1m 45.436s, 102 laps
7. Charles Pic, Lotus, 1m 46.167s, 89 laps
8. Marcus Ericsson, Sauber, 1m 46.253s, 95 laps
9. Max Verstappen, Toro Rosso, 1m 47.194s, 55 laps
10. Stoffel Vandoorne, McLaren, no time, 3 laps