Wehrlein, the team's official reserve driver, hit the front early on and kept himself there by improving his own benchmark several times. The 20-year-old eventually posted a lap of 1m 42.624s to finish just over half a second clear of the chasing pack.
There were further complications for McLaren's interi Honda-powered car, with the team's reserve driver Stoffel Vandoorne able to complete just two untimed laps - one fewer than his day one total.
An electrical issue was discovered just as the team was about to head out in the morning, and it was not until the final hour that the car re-emerged from the garage. When it did, it proved short-lived, with Vandoorne stopping on track on just his second lap to signal an end to the team's test.
"Although this looked like another difficult day, this is just part of the learning experience we expected when we took on the interim car programme," McLaren racing director Eric Boullier said. "I'd rather be ironing out these problems here in Abu Dhabi, than discovering them in Jerez, next February."
With times tumbling in the final 30 minutes, Ferrari protege and GP2 race winner Raffaele Marciello - making his F1 test debut with the Scuderia - leapt into second.
"Today was a dream come true," Marciello said. "For an Italian, to jump into a Ferrari, at an official test no less, is a really strong emotion and I am grateful to the team for giving me this opportunity. This being my first time at the wheel of an F14 T, I had to gradually adapt my driving style, but in general, I felt comfortable and I hope I helped the team gather useful data."
Toro Rosso's 2015 rookie Max Verstappen slotted into third. The Dutchman enjoyed a productive morning - in contrast to the first day, when a suspension failure put him in the barriers - but lost running time in the afternoon with a power unit issue.
Sauber's 2015 signing Marcus Ericsson was fourth fastest and finished the day as the only man to break into triple figures in the lap count, on 112. Caterham's Will Stevens ended the day fifth, having been second fastest before others' late improvements.
Spike Goddard, who took over from GP2 champion Jolyon Palmer at Force India, was fractions down the road in sixth. The Australian F3 racer also trialled a new display system developed by Lewis Hamilton's father Anthony on the top of his VJM07's airbox.
Having set the pace on the first day, Williams ended day two in eighth with test and reserve driver Felipe Nasr, who has signed to race for Sauber in 2015.
"Today was really good day. The focus was on the 2015 tyres and longer runs and we learnt a lot," Nasr reflected. "I have to say a big thank you to the whole team for the opportunities they have given me this year and I wish them all the best for the future."
Lotus, meanwhile, occupied ninth and 10th spots courtesy of GP3 champion Alex Lynn and FIA European Formula Three champion Esteban Ocon, who ran in the afternoon and morning respectively.
Unofficial Wednesday times from Abu Dhabi:
1. Pascal Wehrlein, Mercedes, 1m 42.624s, 96 laps
2. Raffaele Marciello, Ferrari, 1m 43.208s, 91 laps
3. Max Verstappen, Toro Rosso, 1m 43.763s, 78 laps
4. Marcus Ericsson, Sauber, 1m 44.551s, 112 laps
5. Will Stevens, Caterham, 1m 44.888s, 76 laps
6. Spike Goddard, Force India, 1m 44.944s, 89 laps
7. Daniel Ricciardo, Red Bull, 1m 45.151s, 88 laps
8. Felipe Nasr, Williams, 1m 45.937s, 83 laps
9. Alex Lynn, Lotus, 1m 46.168s, 52 laps
10. Esteban Ocon, Lotus, 1m 47.013s, 34 laps
11. Stoffel Vandoorne, McLaren, no time, 2 laps