Kimi Raikkonen kept Ferrari in the mix in third, although the Finn also triggered the red flags and was forced to abandon running prematurely when he spun and tagged the barriers on the exit of Turn 3 late in the afternoon.
Bottas finished the day more than 1s clear of his compatriot, having set a 1m 19.310s - comfortably the fastest time seen so far in testing - early in the morning while running the supersofts on his Mercedes.
WATCH: Ride onboard as Bottas records the quickest lap of the winter so far
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For a while that looked out of reach for the rest of the field, but Tuesday's surprise pacesetter Massa took his Williams to within 0.110s of Bottas after a morning run on the ultrasoft tyre.
Raikkonen set his best time on softs, as did Max Verstappen, who was just 0.026s down the road in fourth. Red Bull didn't enjoy the smoothest day however, opting for a precautionary engine change during lunch and suffering another set-back late on.
Canadian rookie Lance Stroll took over from Massa in the afternoon and didn't put a foot wrong as he racked up 59 laps and guided the FW40 to fifth, just ahead of Lewis Hamilton – who likewise took over driving duties from Bottas in the afternoon but focused on long runs. Particularly of note was the triple world champion's 20-lap stint on ultrasoft tyres.
Renault also split their drivers, with Nico Hulkenberg enjoying a productive morning and Jolyon Palmer a disrupted afternoon as technical gremlins struck. The pair finished seventh and 14th respectively, with Palmer completing just 29 laps.
McLaren and Toro Rosso also lost time in the garage, although the latter recovered from a slow start to rack up 92 laps with Carlos Sainz behind the wheel. Compatriot Fernando Alonso managed 46 in comparison, which included a pre-lunch spin at Turn 1.
The pair were ninth and 12th overall, separated by Haas's Romain Grosjean and Sauber's Pascal Wehrlein – the German driving in the morning before handing over to Marcus Ericsson, who was 13th, for the afternoon.
Sergio Perez meanwhile enjoyed a productive day for Force India as he racked up 100 laps – second only to Verstappen, who managed 102 despite stopping out on track late on.
Bottas's new benchmark lap time is more than half a second faster than the best ever pole lap - set in 2010 by Mark Webber - around the current Barcelona layout, and nearly three seconds faster than Hamilton's pole time last year.