The company's biggest business segment, More Personal Computing -- which includes Windows, devices, gaming and search ads -- produced $9.92 billion in revenue, up 13 percent year over year. The segment came in above the FactSet consensus estimate of $9.25 billion, according to StreetAccount.
The Productivity and Business Processes segment, which includes Office, LinkedIn and Dynamics, came up with $9.01 billion in revenue, which was up 16.8 percent and above the FactSet consensus estimate of $8.73 billion, according to StreetAccount.
Microsoft's Intelligent Cloud segment, containing server products and cloud services, grew 17.3 percent with $7.90 billion in revenue. The results exceeded the $7.68 billion FactSet estimate.
In the fiscal third quarter Microsoft acquired data storage company Avere and gaming start-up PlayFab, and it announced a major reorganization that included the departure of Windows and Devices chief Terry Myerson from the company. The Windows and Devices Group was effectively split up and put inside the Experiences and Devices group (which includes Microsoft's Office 365 and other productivity applications) and the Cloud and Artificial Intelligence Platform group (which includes infrastructure products like Windows Server and the Azure cloud platform).
"We think folding Windows into the new Experiences and Devices division, which is led by a former Office executive, sends a strong signal of the supporting, and not leading, role Windows will likely take in coming years, and we like the continued emphasis on hybrid cloud and [artificial intelligence]," Stifel analysts led by Brad Reback wrote in a Sunday note.
But Windows remains the main revenue contributor for Microsoft's More Personal Computing business segment. One indicator for Windows sales, IDC's PC shipments, was flat year over year in the first quarter of 2018 but better than expected, the Stifel analysts wrote.
Intelligent Cloud contains the Azure public cloud, which competes with Amazon Web Services and represents Microsoft's biggest growth driver overall. Microsoft as usual didn't provide an exact revenue figure for Azure but did say revenue rose 93 percent year over year, which is down sequentially from 98 percent revenue growth. The Stifel analysts said they were expecting growth just over 90 percent, while analysts led by Kirk Materne at Evercore ISI said in a Sunday note they were looking for 82 percent Azure growth.
The deceleration in Azure's revenue growth could have been one factor that caused Microsoft stock to fall immediately after the company reported earnings, Piper Jaffray analyst Alex Zukin told CNBC.
On the call with analysts after the earnings release, Microsoft CEO Satya Nadella said that one Azure service, the Cosmos DB database offering, had more than $100 million in annualized revenue.
Microsoft said its "commercial cloud," which entails Azure, Office 365, Dynamics 365 and other cloud services, had $6 billion in revenue in the fiscal third quarter, up 58 percent year over year and up 13 percent sequentially.
There were 30.6 million Office 365 consumer subscribers in the quarter, up sequentially from 29.2 million. On the Office 365 commercial side, revenue grew 42 percent. The Xbox Live gaming service had 59 million users.
Microsoft's Dynamics 365 revenue increased 65 percent, while LinkedIn revenue grew 37 percent, and Surface revenue rose 32 percent.
The company reported $3.5 billion in capital expenditures, its highest level yet and up 66 percent year over year.
Microsoft stock is up 10 percent since the beginning of 2018.
- CNBC's Josh Lipton contributed to this story.