The Mercedes driver became involved in a fastest lap trade with the Dane and despite being on the slower tyres, Hamilton on the yellow-banded softs while Magnussen attacked on the red super-softs, the Brit ended the session quickest by 0.311s.
Sabastian Vettel had led the early proceedings thanks to quick times on the medium compounds but after not opting to switch to the softer rubber he remained almost a second off the pace of Hamilton.
Elsewhere, it was another frustrating session for new team Haas who completed just one installation lap all morning after discovering 'an anomaly with its turbo charger' which was replaced overnight.
The American team's pain was shared by Sauber who only completed seven laps all morning as Marcus Ericsson made a slow debut in the new C35.
With the majority of teams continuing its individual testing programmes the top three drivers were never seriously contested against, with Williams' Valtteri Bottas taking fourth overall ahead of McLaren-Honda's Jenson Button who set his best time on the soft tyres.
Daniel Ricciardo spent the first half of the morning running pit stop practices before completing long stints on the medium compounds.
Carlos Sainz picked up the rear of a tight midfield pack in sixth as Sergio Perez made a quiet start to his second test despite notching up a healthy bank of 58 laps.
Manor Racing's Pascal Wehrlein, who was only announced to be driving minutes before the morning session, completed the line-up of cars who produced double-figures of timed laps as Sauber and Haas trailed behind.
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