"Rooney's style is different from what we need. That has deprived us of the required fire-power upfront. It was a decision which has been mutually taken by the club and Rooney," said Gomes.
Wilkinson, 33, who will join the team next month, has donned Exeter City colours for six years before moving to Singapore in 2002.
He played for three clubs in Singapore before becoming a Singapore citizen and winning 29 international caps.
The Englishman started his career in Singapore with Woodlands Wellington before joining Geylang United FC and then Singapore Armed Fores FC in 2006.
Wilkinson's five seasons with Singapore Armed Forces were hugely successful, winning four league titles during the club's most successful period.
He also scored the Warrior's first ever goal in the AFC Championships League in a 4-1 away defeat against Shanghai Shenhua in China.