Amla and Philander were named alongside Australia captain Michael Clarke and Sri Lanka batsman Kumar Sangakkara in the short-list for the coveted accolade.
Both players shone during the voting period, which included all international matches between August 4, 2011, and August 12, 2012.
Amla made 915 runs, at an average of 65.35, in 10 Tests over the 12 months, including two centuries and four half-centuries.
He also hit the first triple ton by a South African batsman, contributing an unbeaten 311 runs in the first Test against England at The Oval last month.
Amla proved his value in limited overs matches as well, hitting 419 runs in eight one-day internationals (ODI), with four half-centuries and a ton, at an average of 52.37.
He was less impressive, however, in the explosive Twenty20 version of the game, making 62 runs in five matches at an average of 12.40.
Philander, who made his debut last season in the five-day format, took 56 wickets at a remarkable average of 12.77 in the nine Tests he played during the voting period, bagging 10-wicket hauls against Sri Lanka and New Zealand.
He played only one ODI, taking a single wicket against Sri Lanka in Kimberley in January, and he did not turn out in any T20 International matches.
Amla and Philander were also short-listed for the ICC Test Cricketer of the Year award.
Promising young batsman Richard Levi was nominated for the Twenty20 International Performance of the Year.
Levi smashed an unbeaten 117 runs off only 51 balls in only his second international match, guiding South Africa to an eight-wicket victory over New Zealand in Hamilton in February.
Proteas limited overs captain AB de Villiers and all-rounder Jacques Kallis were both included among the nominees for the ICC Spirit of Cricket accolade, while Kallis and Philander were nominated for the People’s Choice Award.
Meanwhile, South Africans featured prominently in the ICC Test Team of the Year, which was also named on Thursday.
Proteas players filled five of the 12 places up for grabs, including De Villiers who was named as the 12th man.
Also in the team were Amla, Kallis, Philander and fast bowler Dale Steyn who was included in the team for the fifth year in succession.
The next best nation of the six countries represented in the list was England, with three players included.
“Those selected can be justifiably proud of their achievements and well deserving of the recognition they receive as great cricketers of their era,” said ICC chief executive Dave Richardson, a former Proteas wicketkeeper.
“The quality of the Test cricket played over the course of the year has been exceptional and I did not envy the selectors in their task of selecting the best.
“Congratulations to those who have made it. They make a formidable team.”
The ICC Awards ceremony, in its ninth year, will be held in Colombo, Sri Lanka, on September 15.