The French veteran felt Federer's reputation meant he was granted his preference to play in the evening session to avoid the blistering Melbourne heat and offered the Swiss' matches at the last two Australian Opens as evidence.
During the first set, Federer sent a first serve way off the mark.
Federer, who has only failed to reach the semi-finals in the event once in 15 appearances, will still need to beat group leader Kevin Anderson in straight sets on Thursday to be absolutely sure of making it to the weekend. "So I'm very happy that that was the right decision and I was able to show a reaction from my first-round match". "Hopefully I can take my revenge".
Thiem is facing an opening-round exit at the O2 Arena for a third straight season and will need to defeat Nishikori in straight sets to have any chance of progressing.
He will next take on in-form South African, Kevin Anderson, who humbled Nishikori 6-0 6-1 earlier in the day. "Doesn't matter if it's the last one here or not".
Federer grabbed a break in the third game against a nervous-looking Thiem and a second for 5-2 on his way to taking the first set. Novak Djokovic asks Roger Federer question at ATP Finals Novak Djokovic defends youngsters after Federer and Anderson humblings However, even if the 20-time Grand Slam victor does record a comfortable victory, progression would then go down to the percentage of games won between those also tied on two wins. It worked, as another forehand mistake from Thiem put Federer in complete control in the second set.
"It feels good and I am very happy, no game is easy here and I am not used to losing and coming back again, but it was a good challenge and I am happy with the way I played", said Federer after the match.
The 32-year-old won the first 11 games against Nishikori before his relieved opponent finally got on the scoreboard with an angled victor.
"It needs to be said that Roger Federer is a player widely regarded as one of the biggest "box office" athletes in the world", Tiley said.
"I get asked, 'Would you like to play Monday or Tuesday?' some times".
"I got off to a really good start and I think I did a really good job constantly applying the pressure and not letting up".