The World Champion went more than three tenths faster than the Mercedes of George Russell in second place in the session, with Charles Leclerc taking third - albeit almost half a second down on the Red Bull driver's benchmark.
Lewis Hamilton, Sergio Perez and Carlos Sainz followed in behind their team-mates over one-lap pace, with the teams looking at both short and long-run pace through the course of FP2 in Abu Dhabi.
With eight drivers having swapped seats for FP1, the teams mostly filling their mandatory 'young driver' running at the season finale, the full grid was back in play as the sun began to set over Yas Marina.
With FP2 beginning at the same time the race will start on Sunday, the conditions were fully representative for the drivers as they took to the track on Friday evening.
For Verstappen, he was clearly eager to get going - having been sat in his Red Bull cockpit long before the lights went green as he retook his seat for the session, with Red Bull junior Logan Sargeant having replaced him earlier in the day.
The initial medium and hard-tyre runs allowed the field to get their collective eyes in before qualifying simulations got underway, though Hamilton pulled alongside Kevin Magnussen on the back straight to show his displeasure, after he came right up to the back of the Haas under braking for the Turn 6 hairpin, the Dane going much slower than the Mercedes driver anticipated.
But elsewhere, Verstappen was the first of the front-runners to post a lap on soft rubber, his 1:25.449 putting him almost six tenths quicker than Leclerc's quickest effort - despite then complaining of his brake pedal being "very bad" during the lap.
He was able to improve by a further tenth while others remained out on harder compounds, with Mick Schumacher separately urging Haas to check his floor, with his car bouncing its way through several corners - seemingly causing a troubled ride through the long right-hander of Turn 3 in particular.
The Mercedes duo were the last to set representative soft-tyre times and Russell navigated his way through traffic in the final sector to clock a 1:25.487, before Hamilton crossed the line on a 1:25.829 after losing a chunk of time in the last part of the lap, having gone 'purple' in sector one.
As ever in Abu Dhabi, the fading natural light saw the floodlights take over for the second part of FP2, as will be the case in the race this Sunday, with a second qualifying simulation to come before long runs became the focus for the field.
Verstappen improved yet again to a 1:25.146, putting him 0.341s clear of Russell behind as the reigning World Champion opted to take an extra flying run before switching focus to a higher-fuel stint - the lack of FP1 running clearly proving to be no barrier to the Red Bull driver.
With Leclerc third, the Red Bull-Ferrari-Mercedes top three was followed by their team-mates to fill out places four, five and six in FP2, before the Alpine pair of Esteban Ocon and Fernando Alonso, McLaren's Daniel Ricciardo and Alfa Romeo driver Valtteri Bottas rounded out the top 10 in the second half of Friday's practice running.