CLEMSON -- Brandon Thomas was mentally meandering at 11:15 ET Friday night at his family's home in Spartanburg, ready to turn off the TV, trade the couch for his bed and wait another day to find out his future.

Not so fast. The former Clemson offensive lineman's cell buzzed. It was 49ers coach Jim Harbaugh.

"It was crazy. It was a long, long process," Thomas recounted Saturday morning. "We were all getting tired. It was funny, because I was sitting watching it, and I started yawning, saying, I'm tired. It was the last pick, I can't wait to go to bed. Then I get a phone call."

San Francisco's got a reputation as one of the meanest teams in the NFL, translating to appearances in the last two NFC Championship games.

"Offensively, with the addition of (fellow 3rd-round selection) Marcus (Martin) at center and Brandon at the guard-tackle position, those are big guys, big physical football players," 49ers general manager Trent Baalke told local reporters Friday night. "You look at (2nd-round tailback) Carlos (Hyde), another big guy. Big wins. Big wins a lot of football games."

Thomas, a two-time top-squad all-ACC left tackle in 2012 and 2013, became Clemson's first offensive lineman drafted in the first three rounds of the NFL Draft since Joe Bostic in 1979. The selection came as late as it could, as the injured Thomas was taken 100th overall, the final compensatory pick of the third round and Day 2 action.

The night after Clemson's Pro Day in early March, Baalke and a 49ers scout accompanied Thomas, wide receiver Martavis Bryant and cornerback Bashaud Breeland to dinner at J Peters Grill in nearby Anderson.

"I'm excited about it. I feel like they got something from me because they know I'm going to work hard," Thomas said. "I know I'm going to have some great guys around me that are going to teach me the game."

Thomas was a widely-presumed second-round pick, until he tore his ACL April 3 during a pre-draft workout with the Saints. Thomas had successful surgery on his knee April 23, and while Thomas doesn't know for sure if he'll return in 2014, the expectation is he'll sit out the year barring injury to 49ers offensive line starters.

"This injury could be a blessing in disguise," Thomas said, "to take a year to learn from those guys, and get stronger, get better, get my knee stronger. So it's going to be a fun process."

Baalke borrowed the college term "redshirt" to designate his plans with Thomas - the same way the 49ers sat out 2013 fourth-round selection Marcus Lattimore, the former South Carolina running back. Lattimore is hoping to return in 2014.

"He's a great young man," Baalke said of Thomas. "We really had him valued high; he was the highest player on our board once we made our pick. The value was just too high to pass up. We expect him to rehab fine."

Thomas offered counsel to Bryant, Breeland, quarterback Tajh Boyd and his other former teammates still waiting and hoping for a Day 3 selection when the draft resumes Saturday at noon.

"Just stay calm, don't get on edge, just relax. It'll all come out with your dreams come true," Thomas said. "They're all great guys, we had a great program at Clemson, so I know all of us will be satisfied no matter where we go."