The concluding round-robin match at the year-ender had become a straight knockout between the two players after Rafael Nadal had already sealed top spot in Ilie Nastase Group, and Wawrinka looked the sharper as he beat Scotland's world No.2 Murray 7-6 6-4.
Earlier, Nadal emulated Federer by winning a third successive round-robin match, beating fellow Spaniard David Ferrer in three sets.
With Nadal already in the semi-finals and Ferrer going home after two defeats, it could have been a non-event but the packed arena was treated to the longest match of the group stage with Nadal winning 6-7 6-3 6-4 after two hours 37 minutes.
Nadal, twice a runner-up at the Tour Finals, will face Serbia's world No.1 Novak Djokovic in the last four.
It looked as though the Spaniard might be in for an easy ride when he won 10 of the first 11 points, breaking Ferrer twice, but his 33-year-old opponent is renowned as one of the sport's best battlers and he hit back to win a tiebreak.
World No.5 Nadal, who had already beaten fourth-ranked Wawrinka and Murray, buckled down though and levelled the match before breaking the Ferrer serve in the final game of the contest.
Later this morning home favourite Murray and Swiss Wawrinka play off for the runners-up spot which would set up a semi-final against Swiss world number three Federer, the other player with a 100 percent record.