The U.S. tech giant did not want to reveal the size of its investment when contacted by CNBC, but Facebook said in a blog post Tuesday evening that it underscores the company's efforts to help bring small businesses online.
Gojek also declined to disclose the size of Facebook's investment.
"This investment will support Facebook and Gojek's shared goal of empowering businesses and driving financial inclusion across the archipelago," Matt Idema, WhatsApp's chief operating officer, said in the blog post.
"WhatsApp helps small businesses communicate with customers and make sales, and together with Gojek, we believe we can bring millions of people into Indonesia's growing digital economy," Idema said.
Gojek said PayPal also participated in its current funding round along with Facebook. Investments from the two U.S. tech giants as well as other investors will help Gojek ramp up its payments and financial services in the region, the company said.
"By working together, we have the opportunity to achieve something truly unique as we aim to help more businesses to digitise and ensure that many millions more consumers are enjoying the benefits that the digital economy can bring," Gojek co-CEO Andre Soelistyo said in a statement.
Gojek said the collaboration with PayPal would allow users of its digital wallet, GoPay, to access the U.S. firm's network of more than 25 million merchants worldwide.
PayPal did not immediately respond to CNBC's request for comments on the size of its investment.
Facebook's investment into Gojek follows a $5.7 billion investment the social networking giant made in April to India's Jio Platforms — the digital subsidiary of Indian conglomerate Reliance Industries, owned by billionaire Mukesh Ambani.
That investment gave the social network a 9.99% stake in Jio Platforms at a pre-money enterprise value of $65.95 billion.
Both India and Indonesia have large populations that are coming online. They present a valuable opportunity for global tech companies like Facebook to build out their commercial services to micro, small and medium-sized businesses, particularly through the popular messaging service WhatsApp.
Indonesia's internet economy is the largest and fastest-growing in Southeast Asia, according to a frequently-cited industry report last year from Google, Singapore state investor Temasek and consulting firm Bain & Company. It is on track to cross $130 billion by 2025 and is set to benefit from the growing adoption of digital payments, the report said. Southeast Asia's overall internet economy is expected to reach $300 billion by 2025.
Gojek already has a number of prominent backers including Google, Temasek and Chinese tech giant Tencent. The Indonesian start-up has a valuation of $10 billion, according to CB Insights. It raised $1.2 billion of fresh funds in March, reports said.
The company competes with Singapore-headquartered Grab in Southeast Asia across areas such as ride-hailing, payments and food delivery. Both companies say they aim to become the region's top "super app" — where multiple services are bundled into a single application.