PHOENIX - Shortstop Dansby Swanson, the first overall pick in baseball's amateur draft last month, agreed Friday to a $6.5 million signing bonus with the Arizona Diamondbacks just before the deadline for him to reach a deal.

"It was pretty close, like probably the last 10, 15 minutes," said De Jon Watson, the Diamondbacks' senior vice-president of baseball operations.

Swanson's deal was well below the $8,616,900 slotted for the first overall pick under the rules adopted by Major League Baseball and the players' association. The Diamondbacks basically made their final offer and waited to see if Swanson accepted.

"We let them kind of sit on it, think about it," Watson said, "and kept trying to message it to make sure that both sides understood exactly where we were getting down to the last few hours."

Swanson said he wasn't surprised it went down to the wire.

"From everything, I just figured that's how it was going to go," he said in a conference call. "It was pretty stressful but I had faith that everything would get done in an orderly fashion, and it all did."

Draft picks with remaining college eligibility had until 5 p.m. EDT Friday to reach an agreement on a minor league contract. Had a deal not been struck, Swanson would have been eligible to play for Vanderbilt as a senior and Arizona would have received the No. 2 overall pick next June.

Asked if thought about returning to school and re-entering the draft next year, Swanson said, "Yes and no."

"Being No. 1 is obviously the best position you can be at, so it's kind of hard to improve on that," he said. "But you know Vanderbilt is a special place and I'll always hold it near to my heart. It wouldn't be a bad thing to go back just because how everything is operated there."

As a junior at Vanderbilt this season, Swanson hit .325 with 15 home runs, 24 doubles, six triples, 64 RBIs, 16 stolen bases and 76 runs. Swanson was selected most outstanding player in the 2014 College World Series and helped the Commodores reach the Series again this season, where they beat Virginia in the opener of the best-of-three final and then lost two straight. He ranked second in Division I in total bases (175) and third in hits and runs scored.

Swanson, speaking from his home in Georgia, said he would fly to Phoenix on Sunday, stay for a few days to play in the Arizona Rookie League, then join Class A Visalia.

Watson said the Diamondbacks want to make sure Swanson is in baseball shape after his brief layoff.

"You want to make sure when he gets to a full-season club he's ready to compete," Watson said, "and not just go in there cold where he's facing guys who have been playing all summer and are a little bit more advanced as far as pitch recognition, those kind of things. You want to make sure he's ready to go out there and play."

The Diamondbacks also reached a last-minute agreement with 12th-round draft pick Wesley Rodriguez, who will be in Arizona next week to be reassessed by team doctors after tweeting two weeks ago he needed Tommy John surgery.

Rodriguez gave up one earned run in 43 2-3 innings (0.21 ERA) with 92 strikeouts for George Washington High School in New York, where Manny Ramirez went to school. Rodriguez's fastball has been clocked at 99 mph, and he expected to go higher in the draft.