After a couple of years of jockeying, Google has emerged over Microsoft to woo the U.S. Department of Interior into going with a Google Apps partner for the agency’s transition into cloud services.

According to a Twitter post by Andy Blevins, who describes himself on that account as “close to Microsoft and IT decision-makers,” Google Enterprise partner Onix has been awarded a multi-million dollar contract to provide the DOI with email and cloud-based collaboration services.

As alluded to in Blevins’ tweet, the DOI will be transitioning its 88,000 employees to Google’s services. While this is all sunny skies for Google and Onix, Microsoft must be smarting over this one since they were originally slated to be the ones providing the DOI with cloud services.

According to ZDNet, the DOI intended to award Microsoft with the contract in 2010 but Google sued to prevent the deal because it alleged that the DOI acted unfair because it only allowed Microsoft to bid for the competitive contract. Google filed its lawsuit in October, which was only three months after Google Apps for Government was launched, so it’s likely Google just forgot to make its dinner reservation and not so much that they were being purposely excluded. Nevertheless, in the fall of 2011 Google agreed to drop the suit as the agency said it would open up the competition to Google.

Lo and behold, nearly eight months after Google dropped the suit, the DOI announced yesterday that it was going to go with Google instead of Microsoft. ZDNet points out that the price tag for the Google deal, $34.9 million, is considerably less than what the DOI was going to pay Microsoft, $49.3 million. A spokesperson from Google welcomed the contract award, telling WPN, “We’re honored that the Department of the Interior has selected Google Apps for Government, and we look forward to working closely with the DOI to give employees new communication tools.”

Google must be feeling mighty validated over the results of the DOI contract since Microsoft released a comedic yet mordant video called Googlighting in February that painted Google as a fledgling upstart trying to cobble together a passable office suite with Google Docs. The implication in the video was that Google Apps couldn’t hold a candle to Microsoft Office.

When asked for a comment regarding the turn of events, a Microsoft spokesperson said:

Microsoft has a positive, longstanding relationship with the Department of Interior and we are working on a number of enterprise-wide initiatives with the agency. Although we are disappointed by this award, we will engage with our partners and DOI to review and understand the reasons for this decision. Microsoft remains committed to providing our customers with the cloud services that have the performance, security, privacy and other capabilities they expect and deserve.

(This article has been updated to provide the statements from both Microsoft and Google.)