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Arantxa Sanchez Vicario was the only other player from Spain to reach the WTA Finals decider, finishing runner-up to Stefanie Graf in 1993.
But Muguruza exceeded that result as the former world number one proved too strong for Kontaveit at the prestigious year-ending championship.
Muguruza – a two-time grand slam champion – also celebrated her 10th WTA Tour title, having been the only player to beat Kontaveit within the last month following her group-stage success in Guadalajara.
After exchanging breaks in the opening set, Muguruza struck for a 4-3 lead, winning the last four games to seize control midweek.
Kontaveit claimed the early break in the second set as errors started to mount for Muguruza, who eventually found herself 5-3 adrift.
But as Kontaveit served for the set, Muguruza rallied in a dominant display, reeling off four consecutive games like she did in the opener to take home the WTA crown.
Kontaveit – 15/39
Muguruza – 16/25
Kontaveit – 3/6
Muguruza – 2/0
BREAK POINTS WON
Kontaveit – 2/4
Muguruza – 5/11