The Dane had not been a factor at the head of the timesheets until the final 20 minutes, when he bolted on medium tyres and set a 1m33.602s that would prove unmatched for the remainder of the session.
While the afternoon did not yield massive improvements, positions changed hands multiple times as drivers found incremental gains.
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Among them was Paul di Resta, the first of this year's regular drivers to run on Pirelli's new tyres.
The Scot took over from morning pacesetter James Calado in the Force India and immediately improved upon the latter's benchmark.
He was temporarily demoted to second by Red Bull's Antonio Felix da Costa, who was given a full day of running following a late reshuffle that means Mark Webber will no longer test.
Di Resta regained the advantage after a run on Pirelli's soft compound, but his 1m33.774s was eclipsed by Magnussen late on.
Da Costa ended the session third, ahead of Calado and Williams's Daniel Juncadella.
The Spaniard's morning was disrupted for bodywork repairs, and while a clear afternoon lifted his total to 55 laps, he was still some way short of Magnussen's tally of 101.
Johnny Cecotto (Toro Rosso) edged Sauber reserve Robin Frijns in the fight for sixth after his own late improvements.
Frijns set his best time early in the afternoon, putting him fourth at the time, but dropped back as Magnussen and then Cecotto improved.
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Nicolas Prost (Lotus), Davide Rigon (Ferrari) and Alexander Rossi (Caterham) rounded out the top 10.
Rossi's day was brought to a close 30 minutes before time due to a mechanical issue.
Marussia locked out the final two spots through Tio Ellinas and Max Chilton, both of whom were more than three seconds off the pace.
Chilton's afternoon was severely disrupted by an ECU issue that meant he was only able to get out in the final hour, and only able to complete 25 laps in total.
- Paul di Resta